[Met_help] [rt.rap.ucar.edu #98084] History for MET Error - Out of memory reading grib2 data
John Halley Gotway via RT
met_help at ucar.edu
Wed Feb 10 09:06:21 MST 2021
----------------------------------------------------------------
Initial Request
----------------------------------------------------------------
Hello,
My name is Michelle, and I am trying to use the MET software but am running into a memory error and am not sure why or how to fix it. I have tried using the plot_data_plane tool and MODE, but both are giving me the same issue. I am using the supercomputer here at my university, so memory shouldn't be an issue, so I was wondering if this has been an issue for others and if so, what I can do to fix it? I was originally trying to use NetCDF files, but was having trouble with those, so I created grib files from my wrf output instead. I have double checked to ensure my MET and GRIB2C libraries were compiled consistently, so I know that isn't the issue. Any help or guidance would be greatly appreciated!
(base) [spence98 at compute-004 ~]$ mode /home/spence98/spence98/13oct14/control_uh.grb2 /home/spence98/spence98/13oct14/control_uh.grb2 /home/spence98/spence98/13oct14/control_config -outdir /home/spence98/spence98/13oct14/
DEBUG 1: Default Config File: /raid-08/LS/spence98/met-9.1.1/share/met/config/MODEConfig_default
DEBUG 1: Match Config File: /home/spence98/spence98/13oct14/control_config
DEBUG 1: Merge Config File: /home/spence98/spence98/13oct14/control_config
ERROR :
ERROR : Out of memory reading GRIB2 data! Exiting!
ERROR : Check that MET and the GRIB2C library were compiled consistently, either with or without the -D__64BIT__ flag.
ERROR :
Thank you,
Michelle Spencer
Graduate Research Assistant
Atmospheric Science Program
University of Wisconsin-Milwaukee
----------------------------------------------------------------
Complete Ticket History
----------------------------------------------------------------
Subject: MET Error - Out of memory reading grib2 data
From: John Halley Gotway
Time: Wed Dec 30 11:56:14 2020
Hi Michelle,
I see you're having trouble running MET on GRIB2 data. And I think
that
error message is pointing you to the most likely culprit:
*ERROR : Check that MET and the GRIB2C library were compiled
consistently,
either with or without the -D__64BIT__ flag.*
Every time this runtime error has occurred with GRIB2 in the past,
it's
been due to this problem in how the code was compiled. Do you know who
compiled it?
They will need to rerun the ./configure command either with or without
the
-D__64BIT__ flag and rerun make install.
Here's where it's mentioned in the docs:
https://dtcenter.github.io/MET/develop/Users_Guide/installation.html?highlight=64bit
Sorry for this nuisance. I wish the MET configuration step could be
enhanced to automatically handle this situation instead of wasting
users'
time trying to figure it out. Let me know how it goes or if any more
questions arise.
Thanks,
John Halley Gotway
On Wed, Dec 30, 2020 at 11:33 AM Michelle Rose Spencer via RT <
met_help at ucar.edu> wrote:
>
> Wed Dec 30 11:33:12 2020: Request 98084 was acted upon.
> Transaction: Ticket created by spence98 at uwm.edu
> Queue: met_help
> Subject: MET Error - Out of memory reading grib2 data
> Owner: Nobody
> Requestors: spence98 at uwm.edu
> Status: new
> Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=98084 >
>
>
> Hello,
>
> My name is Michelle, and I am trying to use the MET software but am
> running into a memory error and am not sure why or how to fix it. I
have
> tried using the plot_data_plane tool and MODE, but both are giving
me the
> same issue. I am using the supercomputer here at my university, so
memory
> shouldn't be an issue, so I was wondering if this has been an issue
for
> others and if so, what I can do to fix it? I was originally trying
to use
> NetCDF files, but was having trouble with those, so I created grib
files
> from my wrf output instead. I have double checked to ensure my MET
and
> GRIB2C libraries were compiled consistently, so I know that isn't
the
> issue. Any help or guidance would be greatly appreciated!
>
>
> (base) [spence98 at compute-004 ~]$ mode
> /home/spence98/spence98/13oct14/control_uh.grb2
> /home/spence98/spence98/13oct14/control_uh.grb2
> /home/spence98/spence98/13oct14/control_config -outdir
> /home/spence98/spence98/13oct14/
>
> DEBUG 1: Default Config File:
> /raid-08/LS/spence98/met-9.1.1/share/met/config/MODEConfig_default
>
> DEBUG 1: Match Config File:
/home/spence98/spence98/13oct14/control_config
>
> DEBUG 1: Merge Config File:
/home/spence98/spence98/13oct14/control_config
>
> ERROR :
>
> ERROR : Out of memory reading GRIB2 data! Exiting!
>
> ERROR : Check that MET and the GRIB2C library were compiled
consistently,
> either with or without the -D__64BIT__ flag.
>
> ERROR :
>
> Thank you,
>
> Michelle Spencer
> Graduate Research Assistant
> Atmospheric Science Program
> University of Wisconsin-Milwaukee
>
>
>
------------------------------------------------
Subject: MET Error - Out of memory reading grib2 data
From: Michelle Rose Spencer
Time: Wed Dec 30 14:38:12 2020
Hi John,
I compiled the code based off a list of commands my advisor gave me,
which I've included below. I have double checked to make sure that the
grib2c library listed does include the CFLAG -D__64BIT__ flag. I also
just went through and made sure to include the GRIB2CLIB_NAME command
when I ran the ./configure command since the file is named
differently, but this hasn't fixed the error I have. I'd really like
to be able to use this software for my research, so I'm trying to
figure out how to get past this, but my advisor (and myself,
obviously) have never used it before and are out of ideas on what more
to do to fix the error. I'm wondering if it would be worth trying the
NetCDF route again?
wget https://github.com/dtcenter/MET/releases/download/v9.1.1/met-
9.1.1.20201118.tar.gz<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fdtcenter%2FMET%2Freleases%2Fdownload%2Fv9.1.1%2Fmet-
9.1.1.20201118.tar.gz&data=04%7C01%7Cspence98%40uwm.edu%7C4f13af2676ea46f18ac708d89180e2a6%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637419330046745258%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=GF6ghHNs4aDAPcIFxNU4sTlggzrgIhaoGM8df8lClNc%3D&reserved=0>
tar -zxvf met-9.1.1.20201118.tar.gz
cd met-9.1.1
export CXX=icpc
export F77=ifort
export CC=icc
export MET_NETCDF=/raid-11/LS/evans36/software/netcdf
export MET_HDF5=/raid-11/LS/evans36/software/hdf5
export MET_BUFRLIB=/raid-11/LS/evans36/software/bufrlib
export MET_GSL=/raid-11/LS/evans36/software/gsl
export MET_GRIB2CINC=/raid-11/LS/evans36/software/grib2-new/g2clib-
1.6.0
export MET_GRIB2CLIB=/raid-11/LS/evans36/software/grib2-new/g2clib-
1.6.0
export CFLAGS="-D__64BIT__"
./configure --prefix=/raid-08/LS/spence98/met-9.1.1 --enable-grib2
make
make check
make install
Thanks for your help!
Michelle
________________________________
From: John Halley Gotway via RT <met_help at ucar.edu>
Sent: Wednesday, December 30, 2020 12:56 PM
To: Michelle Rose Spencer <spence98 at uwm.edu>
Subject: Re: [rt.rap.ucar.edu #98084] MET Error - Out of memory
reading grib2 data
Hi Michelle,
I see you're having trouble running MET on GRIB2 data. And I think
that
error message is pointing you to the most likely culprit:
*ERROR : Check that MET and the GRIB2C library were compiled
consistently,
either with or without the -D__64BIT__ flag.*
Every time this runtime error has occurred with GRIB2 in the past,
it's
been due to this problem in how the code was compiled. Do you know who
compiled it?
They will need to rerun the ./configure command either with or without
the
-D__64BIT__ flag and rerun make install.
Here's where it's mentioned in the docs:
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdtcenter.github.io%2FMET%2Fdevelop%2FUsers_Guide%2Finstallation.html%3Fhighlight%3D64bit&data=04%7C01%7Cspence98%40uwm.edu%7C9f48b76f9401474e251408d8acf49661%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637449513783161080%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=hqfQ53PNFsCZmbxHJQVuOX17ocGBjleteNp0daRhpoA%3D&reserved=0
Sorry for this nuisance. I wish the MET configuration step could be
enhanced to automatically handle this situation instead of wasting
users'
time trying to figure it out. Let me know how it goes or if any more
questions arise.
Thanks,
John Halley Gotway
On Wed, Dec 30, 2020 at 11:33 AM Michelle Rose Spencer via RT <
met_help at ucar.edu> wrote:
>
> Wed Dec 30 11:33:12 2020: Request 98084 was acted upon.
> Transaction: Ticket created by spence98 at uwm.edu
> Queue: met_help
> Subject: MET Error - Out of memory reading grib2 data
> Owner: Nobody
> Requestors: spence98 at uwm.edu
> Status: new
> Ticket <URL:
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frt.rap.ucar.edu%2Frt%2FTicket%2FDisplay.html%3Fid%3D98084&data=04%7C01%7Cspence98%40uwm.edu%7C9f48b76f9401474e251408d8acf49661%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637449513783161080%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=KDRj2FDF8fQN3c7xpr5LKgloHLi7U2mMdUoa%2BBTS1lU%3D&reserved=0
>
>
>
> Hello,
>
> My name is Michelle, and I am trying to use the MET software but am
> running into a memory error and am not sure why or how to fix it. I
have
> tried using the plot_data_plane tool and MODE, but both are giving
me the
> same issue. I am using the supercomputer here at my university, so
memory
> shouldn't be an issue, so I was wondering if this has been an issue
for
> others and if so, what I can do to fix it? I was originally trying
to use
> NetCDF files, but was having trouble with those, so I created grib
files
> from my wrf output instead. I have double checked to ensure my MET
and
> GRIB2C libraries were compiled consistently, so I know that isn't
the
> issue. Any help or guidance would be greatly appreciated!
>
>
> (base) [spence98 at compute-004 ~]$ mode
> /home/spence98/spence98/13oct14/control_uh.grb2
> /home/spence98/spence98/13oct14/control_uh.grb2
> /home/spence98/spence98/13oct14/control_config -outdir
> /home/spence98/spence98/13oct14/
>
> DEBUG 1: Default Config File:
> /raid-08/LS/spence98/met-9.1.1/share/met/config/MODEConfig_default
>
> DEBUG 1: Match Config File:
/home/spence98/spence98/13oct14/control_config
>
> DEBUG 1: Merge Config File:
/home/spence98/spence98/13oct14/control_config
>
> ERROR :
>
> ERROR : Out of memory reading GRIB2 data! Exiting!
>
> ERROR : Check that MET and the GRIB2C library were compiled
consistently,
> either with or without the -D__64BIT__ flag.
>
> ERROR :
>
> Thank you,
>
> Michelle Spencer
> Graduate Research Assistant
> Atmospheric Science Program
> University of Wisconsin-Milwaukee
>
>
>
------------------------------------------------
Subject: MET Error - Out of memory reading grib2 data
From: John Halley Gotway
Time: Wed Dec 30 15:01:04 2020
Michelle,
Let's try recompiling both the grib2c library and MET WITHOUT that
flag...
(1) Edit your grib2c library compilation.
cd /raid-11/LS/evans36/software/grib2-new/g2clib-1.6.0
(2) Edit the makefile as follows.
Change the INC line to specify the path to the jasper include
directory.
(e.g. on my machine,
INC=-
I/Volumes/d1/projects/MET/MET_external_libs/external_libs/include)
Remove -D__64BIT__ from the CFLAGS line.
(e.g. CFLAGS= -O3 -g -m64 $(INC) $(DEFS))
Reset the library name to just libgrib2c.a.
(e.g. LIB=libgrib2c.a)
(3) Run make to compile it.
(4) Then reconfigure and recompile MET. I usually set the C++ compiler
to
Intel icc, not icpc. So please try that instead.
export CXX=icc
unset CFLAGS
./configure --prefix=/raid-08/LS/spence98/met-9.1.1 --enable-grib2
make clean install
And then re-try your GRIB2 plot_data_plane test.
Any better luck?
Thanks,
John
On Wed, Dec 30, 2020 at 2:38 PM Michelle Rose Spencer via RT <
met_help at ucar.edu> wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=98084 >
>
> Hi John,
>
> I compiled the code based off a list of commands my advisor gave me,
which
> I've included below. I have double checked to make sure that the
grib2c
> library listed does include the CFLAG -D__64BIT__ flag. I also just
went
> through and made sure to include the GRIB2CLIB_NAME command when I
ran the
> ./configure command since the file is named differently, but this
hasn't
> fixed the error I have. I'd really like to be able to use this
software for
> my research, so I'm trying to figure out how to get past this, but
my
> advisor (and myself, obviously) have never used it before and are
out of
> ideas on what more to do to fix the error. I'm wondering if it would
be
> worth trying the NetCDF route again?
>
>
> wget
> https://github.com/dtcenter/MET/releases/download/v9.1.1/met-
9.1.1.20201118.tar.gz
> <
>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fdtcenter%2FMET%2Freleases%2Fdownload%2Fv9.1.1%2Fmet-
9.1.1.20201118.tar.gz&data=04%7C01%7Cspence98%40uwm.edu%7C4f13af2676ea46f18ac708d89180e2a6%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637419330046745258%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=GF6ghHNs4aDAPcIFxNU4sTlggzrgIhaoGM8df8lClNc%3D&reserved=0
> >
>
> tar -zxvf met-9.1.1.20201118.tar.gz
>
> cd met-9.1.1
>
> export CXX=icpc
>
> export F77=ifort
>
> export CC=icc
>
> export MET_NETCDF=/raid-11/LS/evans36/software/netcdf
>
> export MET_HDF5=/raid-11/LS/evans36/software/hdf5
>
> export MET_BUFRLIB=/raid-11/LS/evans36/software/bufrlib
>
> export MET_GSL=/raid-11/LS/evans36/software/gsl
>
> export MET_GRIB2CINC=/raid-11/LS/evans36/software/grib2-new/g2clib-
1.6.0
>
> export MET_GRIB2CLIB=/raid-11/LS/evans36/software/grib2-new/g2clib-
1.6.0
>
> export CFLAGS="-D__64BIT__"
>
> ./configure --prefix=/raid-08/LS/spence98/met-9.1.1 --enable-grib2
>
> make
>
> make check
>
> make install
>
> Thanks for your help!
>
> Michelle
> ________________________________
> From: John Halley Gotway via RT <met_help at ucar.edu>
> Sent: Wednesday, December 30, 2020 12:56 PM
> To: Michelle Rose Spencer <spence98 at uwm.edu>
> Subject: Re: [rt.rap.ucar.edu #98084] MET Error - Out of memory
reading
> grib2 data
>
> Hi Michelle,
>
> I see you're having trouble running MET on GRIB2 data. And I think
that
> error message is pointing you to the most likely culprit:
>
>
> *ERROR : Check that MET and the GRIB2C library were compiled
consistently,
> either with or without the -D__64BIT__ flag.*
>
> Every time this runtime error has occurred with GRIB2 in the past,
it's
> been due to this problem in how the code was compiled. Do you know
who
> compiled it?
> They will need to rerun the ./configure command either with or
without the
> -D__64BIT__ flag and rerun make install.
>
> Here's where it's mentioned in the docs:
>
>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdtcenter.github.io%2FMET%2Fdevelop%2FUsers_Guide%2Finstallation.html%3Fhighlight%3D64bit&data=04%7C01%7Cspence98%40uwm.edu%7C9f48b76f9401474e251408d8acf49661%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637449513783161080%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=hqfQ53PNFsCZmbxHJQVuOX17ocGBjleteNp0daRhpoA%3D&reserved=0
>
> Sorry for this nuisance. I wish the MET configuration step could be
> enhanced to automatically handle this situation instead of wasting
users'
> time trying to figure it out. Let me know how it goes or if any more
> questions arise.
>
> Thanks,
> John Halley Gotway
>
>
> On Wed, Dec 30, 2020 at 11:33 AM Michelle Rose Spencer via RT <
> met_help at ucar.edu> wrote:
>
> >
> > Wed Dec 30 11:33:12 2020: Request 98084 was acted upon.
> > Transaction: Ticket created by spence98 at uwm.edu
> > Queue: met_help
> > Subject: MET Error - Out of memory reading grib2 data
> > Owner: Nobody
> > Requestors: spence98 at uwm.edu
> > Status: new
> > Ticket <URL:
>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frt.rap.ucar.edu%2Frt%2FTicket%2FDisplay.html%3Fid%3D98084&data=04%7C01%7Cspence98%40uwm.edu%7C9f48b76f9401474e251408d8acf49661%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637449513783161080%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=KDRj2FDF8fQN3c7xpr5LKgloHLi7U2mMdUoa%2BBTS1lU%3D&reserved=0
> >
> >
> >
> > Hello,
> >
> > My name is Michelle, and I am trying to use the MET software but
am
> > running into a memory error and am not sure why or how to fix it.
I have
> > tried using the plot_data_plane tool and MODE, but both are giving
me the
> > same issue. I am using the supercomputer here at my university, so
memory
> > shouldn't be an issue, so I was wondering if this has been an
issue for
> > others and if so, what I can do to fix it? I was originally trying
to use
> > NetCDF files, but was having trouble with those, so I created grib
files
> > from my wrf output instead. I have double checked to ensure my MET
and
> > GRIB2C libraries were compiled consistently, so I know that isn't
the
> > issue. Any help or guidance would be greatly appreciated!
> >
> >
> > (base) [spence98 at compute-004 ~]$ mode
> > /home/spence98/spence98/13oct14/control_uh.grb2
> > /home/spence98/spence98/13oct14/control_uh.grb2
> > /home/spence98/spence98/13oct14/control_config -outdir
> > /home/spence98/spence98/13oct14/
> >
> > DEBUG 1: Default Config File:
> > /raid-08/LS/spence98/met-9.1.1/share/met/config/MODEConfig_default
> >
> > DEBUG 1: Match Config File:
> /home/spence98/spence98/13oct14/control_config
> >
> > DEBUG 1: Merge Config File:
> /home/spence98/spence98/13oct14/control_config
> >
> > ERROR :
> >
> > ERROR : Out of memory reading GRIB2 data! Exiting!
> >
> > ERROR : Check that MET and the GRIB2C library were compiled
> consistently,
> > either with or without the -D__64BIT__ flag.
> >
> > ERROR :
> >
> > Thank you,
> >
> > Michelle Spencer
> > Graduate Research Assistant
> > Atmospheric Science Program
> > University of Wisconsin-Milwaukee
> >
> >
> >
>
>
>
------------------------------------------------
Subject: MET Error - Out of memory reading grib2 data
From: Michelle Rose Spencer
Time: Wed Dec 30 16:21:18 2020
Hi John,
Okay, so I went ahead and copied the grib2-new/ directory into my own
directory so I could make changes to it without affecting anyone else
whom may be using that software. I made the changes you suggested and
tried to re-run the plot_data_plane test. I ** think ** that fixed the
memory issue, because it appears to have read the file. However, I am
now getting this message: I apologize for all of the questions, a lot
of this is very new to me.
plot_data_plane: /usr/lib64/libz.so.1: version `ZLIB_1.2.9' not found
(required by /raid-11/LS/evans36/software/grib2-
new//lib/libpng16.so.16)"
I apologize for all of the questions, a lot of this is very new to me,
but I appreciate your help! I'm not sure if I made a mistake in the
reconfiguring/recompiling process or if this is due to a different
issue (like maybe something due to the way I copied over the grib2-new
directory or something?). I may be able to reach out to my advisor at
this point and see if he has ideas now, but I just wanted to give you
the update on the process!
Thank you,
Michelle
________________________________
From: John Halley Gotway via RT <met_help at ucar.edu>
Sent: Wednesday, December 30, 2020 4:01 PM
To: Michelle Rose Spencer <spence98 at uwm.edu>
Subject: Re: [rt.rap.ucar.edu #98084] MET Error - Out of memory
reading grib2 data
Michelle,
Let's try recompiling both the grib2c library and MET WITHOUT that
flag...
(1) Edit your grib2c library compilation.
cd /raid-11/LS/evans36/software/grib2-new/g2clib-1.6.0
(2) Edit the makefile as follows.
Change the INC line to specify the path to the jasper include
directory.
(e.g. on my machine,
INC=-
I/Volumes/d1/projects/MET/MET_external_libs/external_libs/include)
Remove -D__64BIT__ from the CFLAGS line.
(e.g. CFLAGS= -O3 -g -m64 $(INC) $(DEFS))
Reset the library name to just libgrib2c.a.
(e.g. LIB=libgrib2c.a)
(3) Run make to compile it.
(4) Then reconfigure and recompile MET. I usually set the C++ compiler
to
Intel icc, not icpc. So please try that instead.
export CXX=icc
unset CFLAGS
./configure --prefix=/raid-08/LS/spence98/met-9.1.1 --enable-grib2
make clean install
And then re-try your GRIB2 plot_data_plane test.
Any better luck?
Thanks,
John
On Wed, Dec 30, 2020 at 2:38 PM Michelle Rose Spencer via RT <
met_help at ucar.edu> wrote:
>
> <URL:
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frt.rap.ucar.edu%2Frt%2FTicket%2FDisplay.html%3Fid%3D98084&data=04%7C01%7Cspence98%40uwm.edu%7C7ff79bb0b23b4080f79908d8ad0e69d5%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637449624702812532%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=PavI%2BQXp4mGfVSVIOb21C3o%2FQHqHjdz2CzdnLKE4JWc%3D&reserved=0
>
>
> Hi John,
>
> I compiled the code based off a list of commands my advisor gave me,
which
> I've included below. I have double checked to make sure that the
grib2c
> library listed does include the CFLAG -D__64BIT__ flag. I also just
went
> through and made sure to include the GRIB2CLIB_NAME command when I
ran the
> ./configure command since the file is named differently, but this
hasn't
> fixed the error I have. I'd really like to be able to use this
software for
> my research, so I'm trying to figure out how to get past this, but
my
> advisor (and myself, obviously) have never used it before and are
out of
> ideas on what more to do to fix the error. I'm wondering if it would
be
> worth trying the NetCDF route again?
>
>
> wget
>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fdtcenter%2FMET%2Freleases%2Fdownload%2Fv9.1.1%2Fmet-
9.1.1.20201118.tar.gz&data=04%7C01%7Cspence98%40uwm.edu%7C7ff79bb0b23b4080f79908d8ad0e69d5%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637449624702812532%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=f7Ml75uQT%2FoNeaTqODHZH95iCzK4fFk%2BkTDGcF%2FmOMc%3D&reserved=0
> <
>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fdtcenter%2FMET%2Freleases%2Fdownload%2Fv9.1.1%2Fmet-
9.1.1.20201118.tar.gz&data=04%7C01%7Cspence98%40uwm.edu%7C7ff79bb0b23b4080f79908d8ad0e69d5%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637449624702812532%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=f7Ml75uQT%2FoNeaTqODHZH95iCzK4fFk%2BkTDGcF%2FmOMc%3D&reserved=0
> >
>
> tar -zxvf met-9.1.1.20201118.tar.gz
>
> cd met-9.1.1
>
> export CXX=icpc
>
> export F77=ifort
>
> export CC=icc
>
> export MET_NETCDF=/raid-11/LS/evans36/software/netcdf
>
> export MET_HDF5=/raid-11/LS/evans36/software/hdf5
>
> export MET_BUFRLIB=/raid-11/LS/evans36/software/bufrlib
>
> export MET_GSL=/raid-11/LS/evans36/software/gsl
>
> export MET_GRIB2CINC=/raid-11/LS/evans36/software/grib2-new/g2clib-
1.6.0
>
> export MET_GRIB2CLIB=/raid-11/LS/evans36/software/grib2-new/g2clib-
1.6.0
>
> export CFLAGS="-D__64BIT__"
>
> ./configure --prefix=/raid-08/LS/spence98/met-9.1.1 --enable-grib2
>
> make
>
> make check
>
> make install
>
> Thanks for your help!
>
> Michelle
> ________________________________
> From: John Halley Gotway via RT <met_help at ucar.edu>
> Sent: Wednesday, December 30, 2020 12:56 PM
> To: Michelle Rose Spencer <spence98 at uwm.edu>
> Subject: Re: [rt.rap.ucar.edu #98084] MET Error - Out of memory
reading
> grib2 data
>
> Hi Michelle,
>
> I see you're having trouble running MET on GRIB2 data. And I think
that
> error message is pointing you to the most likely culprit:
>
>
> *ERROR : Check that MET and the GRIB2C library were compiled
consistently,
> either with or without the -D__64BIT__ flag.*
>
> Every time this runtime error has occurred with GRIB2 in the past,
it's
> been due to this problem in how the code was compiled. Do you know
who
> compiled it?
> They will need to rerun the ./configure command either with or
without the
> -D__64BIT__ flag and rerun make install.
>
> Here's where it's mentioned in the docs:
>
>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdtcenter.github.io%2FMET%2Fdevelop%2FUsers_Guide%2Finstallation.html%3Fhighlight%3D64bit&data=04%7C01%7Cspence98%40uwm.edu%7C7ff79bb0b23b4080f79908d8ad0e69d5%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637449624702822527%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=MXft8qcDYFTETuDwKzS2H1dOH8WHQTUVaLfy38ye1EQ%3D&reserved=0
>
> Sorry for this nuisance. I wish the MET configuration step could be
> enhanced to automatically handle this situation instead of wasting
users'
> time trying to figure it out. Let me know how it goes or if any more
> questions arise.
>
> Thanks,
> John Halley Gotway
>
>
> On Wed, Dec 30, 2020 at 11:33 AM Michelle Rose Spencer via RT <
> met_help at ucar.edu> wrote:
>
> >
> > Wed Dec 30 11:33:12 2020: Request 98084 was acted upon.
> > Transaction: Ticket created by spence98 at uwm.edu
> > Queue: met_help
> > Subject: MET Error - Out of memory reading grib2 data
> > Owner: Nobody
> > Requestors: spence98 at uwm.edu
> > Status: new
> > Ticket <URL:
>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frt.rap.ucar.edu%2Frt%2FTicket%2FDisplay.html%3Fid%3D98084&data=04%7C01%7Cspence98%40uwm.edu%7C7ff79bb0b23b4080f79908d8ad0e69d5%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637449624702822527%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=fOeCTFCNeJmqo%2BrXWGt49i8zfmvLYUwd5VT%2FJDnm1kk%3D&reserved=0
> >
> >
> >
> > Hello,
> >
> > My name is Michelle, and I am trying to use the MET software but
am
> > running into a memory error and am not sure why or how to fix it.
I have
> > tried using the plot_data_plane tool and MODE, but both are giving
me the
> > same issue. I am using the supercomputer here at my university, so
memory
> > shouldn't be an issue, so I was wondering if this has been an
issue for
> > others and if so, what I can do to fix it? I was originally trying
to use
> > NetCDF files, but was having trouble with those, so I created grib
files
> > from my wrf output instead. I have double checked to ensure my MET
and
> > GRIB2C libraries were compiled consistently, so I know that isn't
the
> > issue. Any help or guidance would be greatly appreciated!
> >
> >
> > (base) [spence98 at compute-004 ~]$ mode
> > /home/spence98/spence98/13oct14/control_uh.grb2
> > /home/spence98/spence98/13oct14/control_uh.grb2
> > /home/spence98/spence98/13oct14/control_config -outdir
> > /home/spence98/spence98/13oct14/
> >
> > DEBUG 1: Default Config File:
> > /raid-08/LS/spence98/met-9.1.1/share/met/config/MODEConfig_default
> >
> > DEBUG 1: Match Config File:
> /home/spence98/spence98/13oct14/control_config
> >
> > DEBUG 1: Merge Config File:
> /home/spence98/spence98/13oct14/control_config
> >
> > ERROR :
> >
> > ERROR : Out of memory reading GRIB2 data! Exiting!
> >
> > ERROR : Check that MET and the GRIB2C library were compiled
> consistently,
> > either with or without the -D__64BIT__ flag.
> >
> > ERROR :
> >
> > Thank you,
> >
> > Michelle Spencer
> > Graduate Research Assistant
> > Atmospheric Science Program
> > University of Wisconsin-Milwaukee
> >
> >
> >
>
>
>
------------------------------------------------
Subject: MET Error - Out of memory reading grib2 data
From: John Halley Gotway
Time: Wed Dec 30 19:47:59 2020
Michelle,
Glad you made progress. Yes, compiling several dependent libraries and
tools can be frustrating! To help, we provided a sample script on the
MET
website we use for compiling MET from scratch. Look at this page and
search
for “sample script”:
http://dtcenter.org/community-code/model-evaluation-tools-met/download
It may be possible to fix the runtime error you’re getting by setting
the
LD_LIBRARY_PATH environment variable to tell the runtime linker where
to
find that library.so.1 file.
You could try running:
locate libz.so.1
And then set:
export LD_LIBRARY_PATH=/directory/containing/it
And then rerun plot_data_plane. Not positive that’ll fix it though.
John
On Wed, Dec 30, 2020 at 4:21 PM Michelle Rose Spencer via RT <
met_help at ucar.edu> wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=98084 >
>
> Hi John,
>
> Okay, so I went ahead and copied the grib2-new/ directory into my
own
> directory so I could make changes to it without affecting anyone
else whom
> may be using that software. I made the changes you suggested and
tried to
> re-run the plot_data_plane test. I ** think ** that fixed the memory
issue,
> because it appears to have read the file. However, I am now getting
this
> message: I apologize for all of the questions, a lot of this is very
new to
> me.
>
>
> plot_data_plane: /usr/lib64/libz.so.1: version `ZLIB_1.2.9' not
found
> (required by /raid-11/LS/evans36/software/grib2-
new//lib/libpng16.so.16)"
>
>
> I apologize for all of the questions, a lot of this is very new to
me, but
> I appreciate your help! I'm not sure if I made a mistake in the
> reconfiguring/recompiling process or if this is due to a different
issue
> (like maybe something due to the way I copied over the grib2-new
directory
> or something?). I may be able to reach out to my advisor at this
point and
> see if he has ideas now, but I just wanted to give you the update on
the
> process!
>
> Thank you,
> Michelle
> ________________________________
> From: John Halley Gotway via RT <met_help at ucar.edu>
> Sent: Wednesday, December 30, 2020 4:01 PM
> To: Michelle Rose Spencer <spence98 at uwm.edu>
> Subject: Re: [rt.rap.ucar.edu #98084] MET Error - Out of memory
reading
> grib2 data
>
> Michelle,
>
> Let's try recompiling both the grib2c library and MET WITHOUT that
flag...
>
> (1) Edit your grib2c library compilation.
> cd /raid-11/LS/evans36/software/grib2-new/g2clib-1.6.0
>
> (2) Edit the makefile as follows.
>
> Change the INC line to specify the path to the jasper include
directory.
> (e.g. on my machine,
> INC=-
I/Volumes/d1/projects/MET/MET_external_libs/external_libs/include)
>
> Remove -D__64BIT__ from the CFLAGS line.
> (e.g. CFLAGS= -O3 -g -m64 $(INC) $(DEFS))
>
> Reset the library name to just libgrib2c.a.
> (e.g. LIB=libgrib2c.a)
>
> (3) Run make to compile it.
>
> (4) Then reconfigure and recompile MET. I usually set the C++
compiler to
> Intel icc, not icpc. So please try that instead.
>
> export CXX=icc
> unset CFLAGS
> ./configure --prefix=/raid-08/LS/spence98/met-9.1.1 --enable-grib2
> make clean install
>
> And then re-try your GRIB2 plot_data_plane test.
>
> Any better luck?
>
> Thanks,
> John
>
>
> On Wed, Dec 30, 2020 at 2:38 PM Michelle Rose Spencer via RT <
> met_help at ucar.edu> wrote:
>
> >
> > <URL:
>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frt.rap.ucar.edu%2Frt%2FTicket%2FDisplay.html%3Fid%3D98084&data=04%7C01%7Cspence98%40uwm.edu%7C7ff79bb0b23b4080f79908d8ad0e69d5%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637449624702812532%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=PavI%2BQXp4mGfVSVIOb21C3o%2FQHqHjdz2CzdnLKE4JWc%3D&reserved=0
> >
> >
> > Hi John,
> >
> > I compiled the code based off a list of commands my advisor gave
me,
> which
> > I've included below. I have double checked to make sure that the
grib2c
> > library listed does include the CFLAG -D__64BIT__ flag. I also
just went
> > through and made sure to include the GRIB2CLIB_NAME command when I
ran
> the
> > ./configure command since the file is named differently, but this
hasn't
> > fixed the error I have. I'd really like to be able to use this
software
> for
> > my research, so I'm trying to figure out how to get past this, but
my
> > advisor (and myself, obviously) have never used it before and are
out of
> > ideas on what more to do to fix the error. I'm wondering if it
would be
> > worth trying the NetCDF route again?
> >
> >
> > wget
> >
>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fdtcenter%2FMET%2Freleases%2Fdownload%2Fv9.1.1%2Fmet-
9.1.1.20201118.tar.gz&data=04%7C01%7Cspence98%40uwm.edu%7C7ff79bb0b23b4080f79908d8ad0e69d5%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637449624702812532%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=f7Ml75uQT%2FoNeaTqODHZH95iCzK4fFk%2BkTDGcF%2FmOMc%3D&reserved=0
> > <
> >
>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fdtcenter%2FMET%2Freleases%2Fdownload%2Fv9.1.1%2Fmet-
9.1.1.20201118.tar.gz&data=04%7C01%7Cspence98%40uwm.edu%7C7ff79bb0b23b4080f79908d8ad0e69d5%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637449624702812532%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=f7Ml75uQT%2FoNeaTqODHZH95iCzK4fFk%2BkTDGcF%2FmOMc%3D&reserved=0
> > >
> >
> > tar -zxvf met-9.1.1.20201118.tar.gz
> >
> > cd met-9.1.1
> >
> > export CXX=icpc
> >
> > export F77=ifort
> >
> > export CC=icc
> >
> > export MET_NETCDF=/raid-11/LS/evans36/software/netcdf
> >
> > export MET_HDF5=/raid-11/LS/evans36/software/hdf5
> >
> > export MET_BUFRLIB=/raid-11/LS/evans36/software/bufrlib
> >
> > export MET_GSL=/raid-11/LS/evans36/software/gsl
> >
> > export MET_GRIB2CINC=/raid-11/LS/evans36/software/grib2-
new/g2clib-1.6.0
> >
> > export MET_GRIB2CLIB=/raid-11/LS/evans36/software/grib2-
new/g2clib-1.6.0
> >
> > export CFLAGS="-D__64BIT__"
> >
> > ./configure --prefix=/raid-08/LS/spence98/met-9.1.1 --enable-grib2
> >
> > make
> >
> > make check
> >
> > make install
> >
> > Thanks for your help!
> >
> > Michelle
> > ________________________________
> > From: John Halley Gotway via RT <met_help at ucar.edu>
> > Sent: Wednesday, December 30, 2020 12:56 PM
> > To: Michelle Rose Spencer <spence98 at uwm.edu>
> > Subject: Re: [rt.rap.ucar.edu #98084] MET Error - Out of memory
reading
> > grib2 data
> >
> > Hi Michelle,
> >
> > I see you're having trouble running MET on GRIB2 data. And I think
that
> > error message is pointing you to the most likely culprit:
> >
> >
> > *ERROR : Check that MET and the GRIB2C library were compiled
> consistently,
> > either with or without the -D__64BIT__ flag.*
> >
> > Every time this runtime error has occurred with GRIB2 in the past,
it's
> > been due to this problem in how the code was compiled. Do you know
who
> > compiled it?
> > They will need to rerun the ./configure command either with or
without
> the
> > -D__64BIT__ flag and rerun make install.
> >
> > Here's where it's mentioned in the docs:
> >
> >
>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdtcenter.github.io%2FMET%2Fdevelop%2FUsers_Guide%2Finstallation.html%3Fhighlight%3D64bit&data=04%7C01%7Cspence98%40uwm.edu%7C7ff79bb0b23b4080f79908d8ad0e69d5%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637449624702822527%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=MXft8qcDYFTETuDwKzS2H1dOH8WHQTUVaLfy38ye1EQ%3D&reserved=0
> >
> > Sorry for this nuisance. I wish the MET configuration step could
be
> > enhanced to automatically handle this situation instead of wasting
users'
> > time trying to figure it out. Let me know how it goes or if any
more
> > questions arise.
> >
> > Thanks,
> > John Halley Gotway
> >
> >
> > On Wed, Dec 30, 2020 at 11:33 AM Michelle Rose Spencer via RT <
> > met_help at ucar.edu> wrote:
> >
> > >
> > > Wed Dec 30 11:33:12 2020: Request 98084 was acted upon.
> > > Transaction: Ticket created by spence98 at uwm.edu
> > > Queue: met_help
> > > Subject: MET Error - Out of memory reading grib2 data
> > > Owner: Nobody
> > > Requestors: spence98 at uwm.edu
> > > Status: new
> > > Ticket <URL:
> >
>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frt.rap.ucar.edu%2Frt%2FTicket%2FDisplay.html%3Fid%3D98084&data=04%7C01%7Cspence98%40uwm.edu%7C7ff79bb0b23b4080f79908d8ad0e69d5%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637449624702822527%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=fOeCTFCNeJmqo%2BrXWGt49i8zfmvLYUwd5VT%2FJDnm1kk%3D&reserved=0
> > >
> > >
> > >
> > > Hello,
> > >
> > > My name is Michelle, and I am trying to use the MET software but
am
> > > running into a memory error and am not sure why or how to fix
it. I
> have
> > > tried using the plot_data_plane tool and MODE, but both are
giving me
> the
> > > same issue. I am using the supercomputer here at my university,
so
> memory
> > > shouldn't be an issue, so I was wondering if this has been an
issue for
> > > others and if so, what I can do to fix it? I was originally
trying to
> use
> > > NetCDF files, but was having trouble with those, so I created
grib
> files
> > > from my wrf output instead. I have double checked to ensure my
MET and
> > > GRIB2C libraries were compiled consistently, so I know that
isn't the
> > > issue. Any help or guidance would be greatly appreciated!
> > >
> > >
> > > (base) [spence98 at compute-004 ~]$ mode
> > > /home/spence98/spence98/13oct14/control_uh.grb2
> > > /home/spence98/spence98/13oct14/control_uh.grb2
> > > /home/spence98/spence98/13oct14/control_config -outdir
> > > /home/spence98/spence98/13oct14/
> > >
> > > DEBUG 1: Default Config File:
> > > /raid-08/LS/spence98/met-
9.1.1/share/met/config/MODEConfig_default
> > >
> > > DEBUG 1: Match Config File:
> > /home/spence98/spence98/13oct14/control_config
> > >
> > > DEBUG 1: Merge Config File:
> > /home/spence98/spence98/13oct14/control_config
> > >
> > > ERROR :
> > >
> > > ERROR : Out of memory reading GRIB2 data! Exiting!
> > >
> > > ERROR : Check that MET and the GRIB2C library were compiled
> > consistently,
> > > either with or without the -D__64BIT__ flag.
> > >
> > > ERROR :
> > >
> > > Thank you,
> > >
> > > Michelle Spencer
> > > Graduate Research Assistant
> > > Atmospheric Science Program
> > > University of Wisconsin-Milwaukee
> > >
> > >
> > >
> >
> >
> >
>
>
>
------------------------------------------------
Subject: MET Error - Out of memory reading grib2 data
From: John Halley Gotway
Time: Thu Jan 07 15:41:17 2021
Hi Michelle,
Just following up on this support ticket. Wondering if you've been
able to
make progress or are you still stuck?
Thanks,
John
On Wed, Dec 30, 2020 at 7:47 PM John Halley Gotway <johnhg at ucar.edu>
wrote:
> Michelle,
>
> Glad you made progress. Yes, compiling several dependent libraries
and
> tools can be frustrating! To help, we provided a sample script on
the MET
> website we use for compiling MET from scratch. Look at this page and
search
> for “sample script”:
>
> http://dtcenter.org/community-code/model-evaluation-tools-
met/download
>
> It may be possible to fix the runtime error you’re getting by
setting the
> LD_LIBRARY_PATH environment variable to tell the runtime linker
where to
> find that library.so.1 file.
>
> You could try running:
> locate libz.so.1
>
> And then set:
> export LD_LIBRARY_PATH=/directory/containing/it
>
> And then rerun plot_data_plane. Not positive that’ll fix it though.
>
> John
>
>
> On Wed, Dec 30, 2020 at 4:21 PM Michelle Rose Spencer via RT <
> met_help at ucar.edu> wrote:
>
>>
>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=98084 >
>>
>> Hi John,
>>
>> Okay, so I went ahead and copied the grib2-new/ directory into my
own
>> directory so I could make changes to it without affecting anyone
else whom
>> may be using that software. I made the changes you suggested and
tried to
>> re-run the plot_data_plane test. I ** think ** that fixed the
memory issue,
>> because it appears to have read the file. However, I am now getting
this
>> message: I apologize for all of the questions, a lot of this is
very new to
>> me.
>>
>>
>> plot_data_plane: /usr/lib64/libz.so.1: version `ZLIB_1.2.9' not
found
>> (required by /raid-11/LS/evans36/software/grib2-
new//lib/libpng16.so.16)"
>>
>>
>> I apologize for all of the questions, a lot of this is very new to
me,
>> but I appreciate your help! I'm not sure if I made a mistake in the
>> reconfiguring/recompiling process or if this is due to a different
issue
>> (like maybe something due to the way I copied over the grib2-new
directory
>> or something?). I may be able to reach out to my advisor at this
point and
>> see if he has ideas now, but I just wanted to give you the update
on the
>> process!
>>
>> Thank you,
>> Michelle
>> ________________________________
>> From: John Halley Gotway via RT <met_help at ucar.edu>
>> Sent: Wednesday, December 30, 2020 4:01 PM
>> To: Michelle Rose Spencer <spence98 at uwm.edu>
>> Subject: Re: [rt.rap.ucar.edu #98084] MET Error - Out of memory
reading
>> grib2 data
>>
>> Michelle,
>>
>> Let's try recompiling both the grib2c library and MET WITHOUT that
flag...
>>
>> (1) Edit your grib2c library compilation.
>> cd /raid-11/LS/evans36/software/grib2-new/g2clib-1.6.0
>>
>> (2) Edit the makefile as follows.
>>
>> Change the INC line to specify the path to the jasper include
directory.
>> (e.g. on my machine,
>> INC=-
I/Volumes/d1/projects/MET/MET_external_libs/external_libs/include)
>>
>> Remove -D__64BIT__ from the CFLAGS line.
>> (e.g. CFLAGS= -O3 -g -m64 $(INC) $(DEFS))
>>
>> Reset the library name to just libgrib2c.a.
>> (e.g. LIB=libgrib2c.a)
>>
>> (3) Run make to compile it.
>>
>> (4) Then reconfigure and recompile MET. I usually set the C++
compiler to
>> Intel icc, not icpc. So please try that instead.
>>
>> export CXX=icc
>> unset CFLAGS
>> ./configure --prefix=/raid-08/LS/spence98/met-9.1.1 --enable-grib2
>> make clean install
>>
>> And then re-try your GRIB2 plot_data_plane test.
>>
>> Any better luck?
>>
>> Thanks,
>> John
>>
>>
>> On Wed, Dec 30, 2020 at 2:38 PM Michelle Rose Spencer via RT <
>> met_help at ucar.edu> wrote:
>>
>> >
>> > <URL:
>>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frt.rap.ucar.edu%2Frt%2FTicket%2FDisplay.html%3Fid%3D98084&data=04%7C01%7Cspence98%40uwm.edu%7C7ff79bb0b23b4080f79908d8ad0e69d5%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637449624702812532%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=PavI%2BQXp4mGfVSVIOb21C3o%2FQHqHjdz2CzdnLKE4JWc%3D&reserved=0
>> >
>> >
>> > Hi John,
>> >
>> > I compiled the code based off a list of commands my advisor gave
me,
>> which
>> > I've included below. I have double checked to make sure that the
grib2c
>> > library listed does include the CFLAG -D__64BIT__ flag. I also
just went
>> > through and made sure to include the GRIB2CLIB_NAME command when
I ran
>> the
>> > ./configure command since the file is named differently, but this
hasn't
>> > fixed the error I have. I'd really like to be able to use this
software
>> for
>> > my research, so I'm trying to figure out how to get past this,
but my
>> > advisor (and myself, obviously) have never used it before and are
out of
>> > ideas on what more to do to fix the error. I'm wondering if it
would be
>> > worth trying the NetCDF route again?
>> >
>> >
>> > wget
>> >
>>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fdtcenter%2FMET%2Freleases%2Fdownload%2Fv9.1.1%2Fmet-
9.1.1.20201118.tar.gz&data=04%7C01%7Cspence98%40uwm.edu%7C7ff79bb0b23b4080f79908d8ad0e69d5%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637449624702812532%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=f7Ml75uQT%2FoNeaTqODHZH95iCzK4fFk%2BkTDGcF%2FmOMc%3D&reserved=0
>> > <
>> >
>>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fdtcenter%2FMET%2Freleases%2Fdownload%2Fv9.1.1%2Fmet-
9.1.1.20201118.tar.gz&data=04%7C01%7Cspence98%40uwm.edu%7C7ff79bb0b23b4080f79908d8ad0e69d5%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637449624702812532%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=f7Ml75uQT%2FoNeaTqODHZH95iCzK4fFk%2BkTDGcF%2FmOMc%3D&reserved=0
>> > >
>> >
>> > tar -zxvf met-9.1.1.20201118.tar.gz
>> >
>> > cd met-9.1.1
>> >
>> > export CXX=icpc
>> >
>> > export F77=ifort
>> >
>> > export CC=icc
>> >
>> > export MET_NETCDF=/raid-11/LS/evans36/software/netcdf
>> >
>> > export MET_HDF5=/raid-11/LS/evans36/software/hdf5
>> >
>> > export MET_BUFRLIB=/raid-11/LS/evans36/software/bufrlib
>> >
>> > export MET_GSL=/raid-11/LS/evans36/software/gsl
>> >
>> > export MET_GRIB2CINC=/raid-11/LS/evans36/software/grib2-
new/g2clib-1.6.0
>> >
>> > export MET_GRIB2CLIB=/raid-11/LS/evans36/software/grib2-
new/g2clib-1.6.0
>> >
>> > export CFLAGS="-D__64BIT__"
>> >
>> > ./configure --prefix=/raid-08/LS/spence98/met-9.1.1 --enable-
grib2
>> >
>> > make
>> >
>> > make check
>> >
>> > make install
>> >
>> > Thanks for your help!
>> >
>> > Michelle
>> > ________________________________
>> > From: John Halley Gotway via RT <met_help at ucar.edu>
>> > Sent: Wednesday, December 30, 2020 12:56 PM
>> > To: Michelle Rose Spencer <spence98 at uwm.edu>
>> > Subject: Re: [rt.rap.ucar.edu #98084] MET Error - Out of memory
reading
>> > grib2 data
>> >
>> > Hi Michelle,
>> >
>> > I see you're having trouble running MET on GRIB2 data. And I
think that
>> > error message is pointing you to the most likely culprit:
>> >
>> >
>> > *ERROR : Check that MET and the GRIB2C library were compiled
>> consistently,
>> > either with or without the -D__64BIT__ flag.*
>> >
>> > Every time this runtime error has occurred with GRIB2 in the
past, it's
>> > been due to this problem in how the code was compiled. Do you
know who
>> > compiled it?
>> > They will need to rerun the ./configure command either with or
without
>> the
>> > -D__64BIT__ flag and rerun make install.
>> >
>> > Here's where it's mentioned in the docs:
>> >
>> >
>>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdtcenter.github.io%2FMET%2Fdevelop%2FUsers_Guide%2Finstallation.html%3Fhighlight%3D64bit&data=04%7C01%7Cspence98%40uwm.edu%7C7ff79bb0b23b4080f79908d8ad0e69d5%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637449624702822527%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=MXft8qcDYFTETuDwKzS2H1dOH8WHQTUVaLfy38ye1EQ%3D&reserved=0
>> >
>> > Sorry for this nuisance. I wish the MET configuration step could
be
>> > enhanced to automatically handle this situation instead of
wasting
>> users'
>> > time trying to figure it out. Let me know how it goes or if any
more
>> > questions arise.
>> >
>> > Thanks,
>> > John Halley Gotway
>> >
>> >
>> > On Wed, Dec 30, 2020 at 11:33 AM Michelle Rose Spencer via RT <
>> > met_help at ucar.edu> wrote:
>> >
>> > >
>> > > Wed Dec 30 11:33:12 2020: Request 98084 was acted upon.
>> > > Transaction: Ticket created by spence98 at uwm.edu
>> > > Queue: met_help
>> > > Subject: MET Error - Out of memory reading grib2 data
>> > > Owner: Nobody
>> > > Requestors: spence98 at uwm.edu
>> > > Status: new
>> > > Ticket <URL:
>> >
>>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frt.rap.ucar.edu%2Frt%2FTicket%2FDisplay.html%3Fid%3D98084&data=04%7C01%7Cspence98%40uwm.edu%7C7ff79bb0b23b4080f79908d8ad0e69d5%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637449624702822527%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=fOeCTFCNeJmqo%2BrXWGt49i8zfmvLYUwd5VT%2FJDnm1kk%3D&reserved=0
>> > >
>> > >
>> > >
>> > > Hello,
>> > >
>> > > My name is Michelle, and I am trying to use the MET software
but am
>> > > running into a memory error and am not sure why or how to fix
it. I
>> have
>> > > tried using the plot_data_plane tool and MODE, but both are
giving me
>> the
>> > > same issue. I am using the supercomputer here at my university,
so
>> memory
>> > > shouldn't be an issue, so I was wondering if this has been an
issue
>> for
>> > > others and if so, what I can do to fix it? I was originally
trying to
>> use
>> > > NetCDF files, but was having trouble with those, so I created
grib
>> files
>> > > from my wrf output instead. I have double checked to ensure my
MET and
>> > > GRIB2C libraries were compiled consistently, so I know that
isn't the
>> > > issue. Any help or guidance would be greatly appreciated!
>> > >
>> > >
>> > > (base) [spence98 at compute-004 ~]$ mode
>> > > /home/spence98/spence98/13oct14/control_uh.grb2
>> > > /home/spence98/spence98/13oct14/control_uh.grb2
>> > > /home/spence98/spence98/13oct14/control_config -outdir
>> > > /home/spence98/spence98/13oct14/
>> > >
>> > > DEBUG 1: Default Config File:
>> > > /raid-08/LS/spence98/met-
9.1.1/share/met/config/MODEConfig_default
>> > >
>> > > DEBUG 1: Match Config File:
>> > /home/spence98/spence98/13oct14/control_config
>> > >
>> > > DEBUG 1: Merge Config File:
>> > /home/spence98/spence98/13oct14/control_config
>> > >
>> > > ERROR :
>> > >
>> > > ERROR : Out of memory reading GRIB2 data! Exiting!
>> > >
>> > > ERROR : Check that MET and the GRIB2C library were compiled
>> > consistently,
>> > > either with or without the -D__64BIT__ flag.
>> > >
>> > > ERROR :
>> > >
>> > > Thank you,
>> > >
>> > > Michelle Spencer
>> > > Graduate Research Assistant
>> > > Atmospheric Science Program
>> > > University of Wisconsin-Milwaukee
>> > >
>> > >
>> > >
>> >
>> >
>> >
>>
>>
>>
------------------------------------------------
Subject: MET Error - Out of memory reading grib2 data
From: Michelle Rose Spencer
Time: Fri Jan 08 18:30:19 2021
Hello John,
I am currently still stuck. Per my advisor's suggestion I am
recompiling the necessary codes within my own directory so that I can
hopefully get past the runtime error I was having the last time we
spoke. With AMS preparations and such this week, I haven't been 100%
on top of it, so I apologize for not getting back with you right away.
I did notice through the process I'm going through right now that the
ZLIB version I was using was not the same as what MET was looking for,
so I have downloaded the different version. My hope is that once I
recompile everything within my own directories and have the different
ZLIB version that it will work out and I will be able to move forward
with my plotting and analyses!
I'll keep you posted!
Michelle
________________________________
From: John Halley Gotway via RT <met_help at ucar.edu>
Sent: Thursday, January 7, 2021 4:41 PM
To: Michelle Rose Spencer <spence98 at uwm.edu>
Subject: Re: [rt.rap.ucar.edu #98084] MET Error - Out of memory
reading grib2 data
Hi Michelle,
Just following up on this support ticket. Wondering if you've been
able to
make progress or are you still stuck?
Thanks,
John
On Wed, Dec 30, 2020 at 7:47 PM John Halley Gotway <johnhg at ucar.edu>
wrote:
> Michelle,
>
> Glad you made progress. Yes, compiling several dependent libraries
and
> tools can be frustrating! To help, we provided a sample script on
the MET
> website we use for compiling MET from scratch. Look at this page and
search
> for “sample script”:
>
>
https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdtcenter.org%2Fcommunity-
code%2Fmodel-evaluation-tools-
met%2Fdownload&data=04%7C01%7Cspence98%40uwm.edu%7C488c475c870d46ff8b1c08d8b35d59e4%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637456560832344640%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=lNGfIDGr2jkdLWeW2vUU5UISn%2FNSn2%2FJ1mI%2BNBFySnQ%3D&reserved=0
>
> It may be possible to fix the runtime error you’re getting by
setting the
> LD_LIBRARY_PATH environment variable to tell the runtime linker
where to
> find that library.so.1 file.
>
> You could try running:
> locate libz.so.1
>
> And then set:
> export LD_LIBRARY_PATH=/directory/containing/it
>
> And then rerun plot_data_plane. Not positive that’ll fix it though.
>
> John
>
>
> On Wed, Dec 30, 2020 at 4:21 PM Michelle Rose Spencer via RT <
> met_help at ucar.edu> wrote:
>
>>
>> <URL:
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frt.rap.ucar.edu%2Frt%2FTicket%2FDisplay.html%3Fid%3D98084&data=04%7C01%7Cspence98%40uwm.edu%7C488c475c870d46ff8b1c08d8b35d59e4%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637456560832344640%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Y2DkIY7ZtvVC35XbitwcCDqb4NF%2F1F1WhnGoCrJ%2BiSM%3D&reserved=0
>
>>
>> Hi John,
>>
>> Okay, so I went ahead and copied the grib2-new/ directory into my
own
>> directory so I could make changes to it without affecting anyone
else whom
>> may be using that software. I made the changes you suggested and
tried to
>> re-run the plot_data_plane test. I ** think ** that fixed the
memory issue,
>> because it appears to have read the file. However, I am now getting
this
>> message: I apologize for all of the questions, a lot of this is
very new to
>> me.
>>
>>
>> plot_data_plane: /usr/lib64/libz.so.1: version `ZLIB_1.2.9' not
found
>> (required by /raid-11/LS/evans36/software/grib2-
new//lib/libpng16.so.16)"
>>
>>
>> I apologize for all of the questions, a lot of this is very new to
me,
>> but I appreciate your help! I'm not sure if I made a mistake in the
>> reconfiguring/recompiling process or if this is due to a different
issue
>> (like maybe something due to the way I copied over the grib2-new
directory
>> or something?). I may be able to reach out to my advisor at this
point and
>> see if he has ideas now, but I just wanted to give you the update
on the
>> process!
>>
>> Thank you,
>> Michelle
>> ________________________________
>> From: John Halley Gotway via RT <met_help at ucar.edu>
>> Sent: Wednesday, December 30, 2020 4:01 PM
>> To: Michelle Rose Spencer <spence98 at uwm.edu>
>> Subject: Re: [rt.rap.ucar.edu #98084] MET Error - Out of memory
reading
>> grib2 data
>>
>> Michelle,
>>
>> Let's try recompiling both the grib2c library and MET WITHOUT that
flag...
>>
>> (1) Edit your grib2c library compilation.
>> cd /raid-11/LS/evans36/software/grib2-new/g2clib-1.6.0
>>
>> (2) Edit the makefile as follows.
>>
>> Change the INC line to specify the path to the jasper include
directory.
>> (e.g. on my machine,
>> INC=-
I/Volumes/d1/projects/MET/MET_external_libs/external_libs/include)
>>
>> Remove -D__64BIT__ from the CFLAGS line.
>> (e.g. CFLAGS= -O3 -g -m64 $(INC) $(DEFS))
>>
>> Reset the library name to just libgrib2c.a.
>> (e.g. LIB=libgrib2c.a)
>>
>> (3) Run make to compile it.
>>
>> (4) Then reconfigure and recompile MET. I usually set the C++
compiler to
>> Intel icc, not icpc. So please try that instead.
>>
>> export CXX=icc
>> unset CFLAGS
>> ./configure --prefix=/raid-08/LS/spence98/met-9.1.1 --enable-grib2
>> make clean install
>>
>> And then re-try your GRIB2 plot_data_plane test.
>>
>> Any better luck?
>>
>> Thanks,
>> John
>>
>>
>> On Wed, Dec 30, 2020 at 2:38 PM Michelle Rose Spencer via RT <
>> met_help at ucar.edu> wrote:
>>
>> >
>> > <URL:
>>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frt.rap.ucar.edu%2Frt%2FTicket%2FDisplay.html%3Fid%3D98084&data=04%7C01%7Cspence98%40uwm.edu%7C488c475c870d46ff8b1c08d8b35d59e4%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637456560832344640%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Y2DkIY7ZtvVC35XbitwcCDqb4NF%2F1F1WhnGoCrJ%2BiSM%3D&reserved=0
>> >
>> >
>> > Hi John,
>> >
>> > I compiled the code based off a list of commands my advisor gave
me,
>> which
>> > I've included below. I have double checked to make sure that the
grib2c
>> > library listed does include the CFLAG -D__64BIT__ flag. I also
just went
>> > through and made sure to include the GRIB2CLIB_NAME command when
I ran
>> the
>> > ./configure command since the file is named differently, but this
hasn't
>> > fixed the error I have. I'd really like to be able to use this
software
>> for
>> > my research, so I'm trying to figure out how to get past this,
but my
>> > advisor (and myself, obviously) have never used it before and are
out of
>> > ideas on what more to do to fix the error. I'm wondering if it
would be
>> > worth trying the NetCDF route again?
>> >
>> >
>> > wget
>> >
>>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fdtcenter%2FMET%2Freleases%2Fdownload%2Fv9.1.1%2Fmet-
9.1.1.20201118.tar.gz&data=04%7C01%7Cspence98%40uwm.edu%7C488c475c870d46ff8b1c08d8b35d59e4%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637456560832354631%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=dhLnwC%2BQF%2BUuXluqhT7LppNGvGVvoLh04QeqyFm5w3U%3D&reserved=0
>> > <
>> >
>>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fdtcenter%2FMET%2Freleases%2Fdownload%2Fv9.1.1%2Fmet-
9.1.1.20201118.tar.gz&data=04%7C01%7Cspence98%40uwm.edu%7C488c475c870d46ff8b1c08d8b35d59e4%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637456560832354631%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=dhLnwC%2BQF%2BUuXluqhT7LppNGvGVvoLh04QeqyFm5w3U%3D&reserved=0
>> > >
>> >
>> > tar -zxvf met-9.1.1.20201118.tar.gz
>> >
>> > cd met-9.1.1
>> >
>> > export CXX=icpc
>> >
>> > export F77=ifort
>> >
>> > export CC=icc
>> >
>> > export MET_NETCDF=/raid-11/LS/evans36/software/netcdf
>> >
>> > export MET_HDF5=/raid-11/LS/evans36/software/hdf5
>> >
>> > export MET_BUFRLIB=/raid-11/LS/evans36/software/bufrlib
>> >
>> > export MET_GSL=/raid-11/LS/evans36/software/gsl
>> >
>> > export MET_GRIB2CINC=/raid-11/LS/evans36/software/grib2-
new/g2clib-1.6.0
>> >
>> > export MET_GRIB2CLIB=/raid-11/LS/evans36/software/grib2-
new/g2clib-1.6.0
>> >
>> > export CFLAGS="-D__64BIT__"
>> >
>> > ./configure --prefix=/raid-08/LS/spence98/met-9.1.1 --enable-
grib2
>> >
>> > make
>> >
>> > make check
>> >
>> > make install
>> >
>> > Thanks for your help!
>> >
>> > Michelle
>> > ________________________________
>> > From: John Halley Gotway via RT <met_help at ucar.edu>
>> > Sent: Wednesday, December 30, 2020 12:56 PM
>> > To: Michelle Rose Spencer <spence98 at uwm.edu>
>> > Subject: Re: [rt.rap.ucar.edu #98084] MET Error - Out of memory
reading
>> > grib2 data
>> >
>> > Hi Michelle,
>> >
>> > I see you're having trouble running MET on GRIB2 data. And I
think that
>> > error message is pointing you to the most likely culprit:
>> >
>> >
>> > *ERROR : Check that MET and the GRIB2C library were compiled
>> consistently,
>> > either with or without the -D__64BIT__ flag.*
>> >
>> > Every time this runtime error has occurred with GRIB2 in the
past, it's
>> > been due to this problem in how the code was compiled. Do you
know who
>> > compiled it?
>> > They will need to rerun the ./configure command either with or
without
>> the
>> > -D__64BIT__ flag and rerun make install.
>> >
>> > Here's where it's mentioned in the docs:
>> >
>> >
>>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdtcenter.github.io%2FMET%2Fdevelop%2FUsers_Guide%2Finstallation.html%3Fhighlight%3D64bit&data=04%7C01%7Cspence98%40uwm.edu%7C488c475c870d46ff8b1c08d8b35d59e4%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637456560832354631%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=oXzdccWx1I81OyQQ7cDbVxyJUCjy0tfq5XrtDxWQL0o%3D&reserved=0
>> >
>> > Sorry for this nuisance. I wish the MET configuration step could
be
>> > enhanced to automatically handle this situation instead of
wasting
>> users'
>> > time trying to figure it out. Let me know how it goes or if any
more
>> > questions arise.
>> >
>> > Thanks,
>> > John Halley Gotway
>> >
>> >
>> > On Wed, Dec 30, 2020 at 11:33 AM Michelle Rose Spencer via RT <
>> > met_help at ucar.edu> wrote:
>> >
>> > >
>> > > Wed Dec 30 11:33:12 2020: Request 98084 was acted upon.
>> > > Transaction: Ticket created by spence98 at uwm.edu
>> > > Queue: met_help
>> > > Subject: MET Error - Out of memory reading grib2 data
>> > > Owner: Nobody
>> > > Requestors: spence98 at uwm.edu
>> > > Status: new
>> > > Ticket <URL:
>> >
>>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frt.rap.ucar.edu%2Frt%2FTicket%2FDisplay.html%3Fid%3D98084&data=04%7C01%7Cspence98%40uwm.edu%7C488c475c870d46ff8b1c08d8b35d59e4%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637456560832354631%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=szBYOSxGhYJRXJGtvXYf0JsrMKuaImw0HE1AIFmlhkk%3D&reserved=0
>> > >
>> > >
>> > >
>> > > Hello,
>> > >
>> > > My name is Michelle, and I am trying to use the MET software
but am
>> > > running into a memory error and am not sure why or how to fix
it. I
>> have
>> > > tried using the plot_data_plane tool and MODE, but both are
giving me
>> the
>> > > same issue. I am using the supercomputer here at my university,
so
>> memory
>> > > shouldn't be an issue, so I was wondering if this has been an
issue
>> for
>> > > others and if so, what I can do to fix it? I was originally
trying to
>> use
>> > > NetCDF files, but was having trouble with those, so I created
grib
>> files
>> > > from my wrf output instead. I have double checked to ensure my
MET and
>> > > GRIB2C libraries were compiled consistently, so I know that
isn't the
>> > > issue. Any help or guidance would be greatly appreciated!
>> > >
>> > >
>> > > (base) [spence98 at compute-004 ~]$ mode
>> > > /home/spence98/spence98/13oct14/control_uh.grb2
>> > > /home/spence98/spence98/13oct14/control_uh.grb2
>> > > /home/spence98/spence98/13oct14/control_config -outdir
>> > > /home/spence98/spence98/13oct14/
>> > >
>> > > DEBUG 1: Default Config File:
>> > > /raid-08/LS/spence98/met-
9.1.1/share/met/config/MODEConfig_default
>> > >
>> > > DEBUG 1: Match Config File:
>> > /home/spence98/spence98/13oct14/control_config
>> > >
>> > > DEBUG 1: Merge Config File:
>> > /home/spence98/spence98/13oct14/control_config
>> > >
>> > > ERROR :
>> > >
>> > > ERROR : Out of memory reading GRIB2 data! Exiting!
>> > >
>> > > ERROR : Check that MET and the GRIB2C library were compiled
>> > consistently,
>> > > either with or without the -D__64BIT__ flag.
>> > >
>> > > ERROR :
>> > >
>> > > Thank you,
>> > >
>> > > Michelle Spencer
>> > > Graduate Research Assistant
>> > > Atmospheric Science Program
>> > > University of Wisconsin-Milwaukee
>> > >
>> > >
>> > >
>> >
>> >
>> >
>>
>>
>>
------------------------------------------------
Subject: MET Error - Out of memory reading grib2 data
From: John Halley Gotway
Time: Fri Jan 08 23:31:58 2021
Michelle,
OK, thanks for the update. Sorry to hear that it's causing so much
trouble.
I really do think that that -D__64BIT__ GRIB2C flag is the source of
this
runtime error.
If you are trying to recompile *everything* yourself, please do take a
look
at the script named "compile_MET_all" on the Downloads page:
http://dtcenter.org/community-code/model-evaluation-tools-met/download
My colleague, Julie Prestopnik (who's also on MET-Help) wrote that
script
and uses it to compile MET on several different NCAR and NOAA
machines.
She'd be able to answer any questions you may have about it.
Thanks,
John
On Fri, Jan 8, 2021 at 6:30 PM Michelle Rose Spencer via RT <
met_help at ucar.edu> wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=98084 >
>
> Hello John,
>
> I am currently still stuck. Per my advisor's suggestion I am
recompiling
> the necessary codes within my own directory so that I can hopefully
get
> past the runtime error I was having the last time we spoke. With AMS
> preparations and such this week, I haven't been 100% on top of it,
so I
> apologize for not getting back with you right away.
>
> I did notice through the process I'm going through right now that
the ZLIB
> version I was using was not the same as what MET was looking for, so
I have
> downloaded the different version. My hope is that once I recompile
> everything within my own directories and have the different ZLIB
version
> that it will work out and I will be able to move forward with my
plotting
> and analyses!
>
> I'll keep you posted!
> Michelle
> ________________________________
> From: John Halley Gotway via RT <met_help at ucar.edu>
> Sent: Thursday, January 7, 2021 4:41 PM
> To: Michelle Rose Spencer <spence98 at uwm.edu>
> Subject: Re: [rt.rap.ucar.edu #98084] MET Error - Out of memory
reading
> grib2 data
>
> Hi Michelle,
>
> Just following up on this support ticket. Wondering if you've been
able to
> make progress or are you still stuck?
>
> Thanks,
> John
>
> On Wed, Dec 30, 2020 at 7:47 PM John Halley Gotway <johnhg at ucar.edu>
> wrote:
>
> > Michelle,
> >
> > Glad you made progress. Yes, compiling several dependent libraries
and
> > tools can be frustrating! To help, we provided a sample script on
the MET
> > website we use for compiling MET from scratch. Look at this page
and
> search
> > for “sample script”:
> >
> >
>
https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdtcenter.org%2Fcommunity-
code%2Fmodel-evaluation-tools-
met%2Fdownload&data=04%7C01%7Cspence98%40uwm.edu%7C488c475c870d46ff8b1c08d8b35d59e4%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637456560832344640%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=lNGfIDGr2jkdLWeW2vUU5UISn%2FNSn2%2FJ1mI%2BNBFySnQ%3D&reserved=0
> >
> > It may be possible to fix the runtime error you’re getting by
setting the
> > LD_LIBRARY_PATH environment variable to tell the runtime linker
where to
> > find that library.so.1 file.
> >
> > You could try running:
> > locate libz.so.1
> >
> > And then set:
> > export LD_LIBRARY_PATH=/directory/containing/it
> >
> > And then rerun plot_data_plane. Not positive that’ll fix it
though.
> >
> > John
> >
> >
> > On Wed, Dec 30, 2020 at 4:21 PM Michelle Rose Spencer via RT <
> > met_help at ucar.edu> wrote:
> >
> >>
> >> <URL:
>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frt.rap.ucar.edu%2Frt%2FTicket%2FDisplay.html%3Fid%3D98084&data=04%7C01%7Cspence98%40uwm.edu%7C488c475c870d46ff8b1c08d8b35d59e4%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637456560832344640%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Y2DkIY7ZtvVC35XbitwcCDqb4NF%2F1F1WhnGoCrJ%2BiSM%3D&reserved=0
> >
> >>
> >> Hi John,
> >>
> >> Okay, so I went ahead and copied the grib2-new/ directory into my
own
> >> directory so I could make changes to it without affecting anyone
else
> whom
> >> may be using that software. I made the changes you suggested and
tried
> to
> >> re-run the plot_data_plane test. I ** think ** that fixed the
memory
> issue,
> >> because it appears to have read the file. However, I am now
getting this
> >> message: I apologize for all of the questions, a lot of this is
very
> new to
> >> me.
> >>
> >>
> >> plot_data_plane: /usr/lib64/libz.so.1: version `ZLIB_1.2.9' not
found
> >> (required by
> /raid-11/LS/evans36/software/grib2-new//lib/libpng16.so.16)"
> >>
> >>
> >> I apologize for all of the questions, a lot of this is very new
to me,
> >> but I appreciate your help! I'm not sure if I made a mistake in
the
> >> reconfiguring/recompiling process or if this is due to a
different issue
> >> (like maybe something due to the way I copied over the grib2-new
> directory
> >> or something?). I may be able to reach out to my advisor at this
point
> and
> >> see if he has ideas now, but I just wanted to give you the update
on the
> >> process!
> >>
> >> Thank you,
> >> Michelle
> >> ________________________________
> >> From: John Halley Gotway via RT <met_help at ucar.edu>
> >> Sent: Wednesday, December 30, 2020 4:01 PM
> >> To: Michelle Rose Spencer <spence98 at uwm.edu>
> >> Subject: Re: [rt.rap.ucar.edu #98084] MET Error - Out of memory
reading
> >> grib2 data
> >>
> >> Michelle,
> >>
> >> Let's try recompiling both the grib2c library and MET WITHOUT
that
> flag...
> >>
> >> (1) Edit your grib2c library compilation.
> >> cd /raid-11/LS/evans36/software/grib2-new/g2clib-1.6.0
> >>
> >> (2) Edit the makefile as follows.
> >>
> >> Change the INC line to specify the path to the jasper include
directory.
> >> (e.g. on my machine,
> >> INC=-
I/Volumes/d1/projects/MET/MET_external_libs/external_libs/include)
> >>
> >> Remove -D__64BIT__ from the CFLAGS line.
> >> (e.g. CFLAGS= -O3 -g -m64 $(INC) $(DEFS))
> >>
> >> Reset the library name to just libgrib2c.a.
> >> (e.g. LIB=libgrib2c.a)
> >>
> >> (3) Run make to compile it.
> >>
> >> (4) Then reconfigure and recompile MET. I usually set the C++
compiler
> to
> >> Intel icc, not icpc. So please try that instead.
> >>
> >> export CXX=icc
> >> unset CFLAGS
> >> ./configure --prefix=/raid-08/LS/spence98/met-9.1.1 --enable-
grib2
> >> make clean install
> >>
> >> And then re-try your GRIB2 plot_data_plane test.
> >>
> >> Any better luck?
> >>
> >> Thanks,
> >> John
> >>
> >>
> >> On Wed, Dec 30, 2020 at 2:38 PM Michelle Rose Spencer via RT <
> >> met_help at ucar.edu> wrote:
> >>
> >> >
> >> > <URL:
> >>
>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frt.rap.ucar.edu%2Frt%2FTicket%2FDisplay.html%3Fid%3D98084&data=04%7C01%7Cspence98%40uwm.edu%7C488c475c870d46ff8b1c08d8b35d59e4%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637456560832344640%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Y2DkIY7ZtvVC35XbitwcCDqb4NF%2F1F1WhnGoCrJ%2BiSM%3D&reserved=0
> >> >
> >> >
> >> > Hi John,
> >> >
> >> > I compiled the code based off a list of commands my advisor
gave me,
> >> which
> >> > I've included below. I have double checked to make sure that
the
> grib2c
> >> > library listed does include the CFLAG -D__64BIT__ flag. I also
just
> went
> >> > through and made sure to include the GRIB2CLIB_NAME command
when I ran
> >> the
> >> > ./configure command since the file is named differently, but
this
> hasn't
> >> > fixed the error I have. I'd really like to be able to use this
> software
> >> for
> >> > my research, so I'm trying to figure out how to get past this,
but my
> >> > advisor (and myself, obviously) have never used it before and
are out
> of
> >> > ideas on what more to do to fix the error. I'm wondering if it
would
> be
> >> > worth trying the NetCDF route again?
> >> >
> >> >
> >> > wget
> >> >
> >>
>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fdtcenter%2FMET%2Freleases%2Fdownload%2Fv9.1.1%2Fmet-
9.1.1.20201118.tar.gz&data=04%7C01%7Cspence98%40uwm.edu%7C488c475c870d46ff8b1c08d8b35d59e4%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637456560832354631%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=dhLnwC%2BQF%2BUuXluqhT7LppNGvGVvoLh04QeqyFm5w3U%3D&reserved=0
> >> > <
> >> >
> >>
>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fdtcenter%2FMET%2Freleases%2Fdownload%2Fv9.1.1%2Fmet-
9.1.1.20201118.tar.gz&data=04%7C01%7Cspence98%40uwm.edu%7C488c475c870d46ff8b1c08d8b35d59e4%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637456560832354631%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=dhLnwC%2BQF%2BUuXluqhT7LppNGvGVvoLh04QeqyFm5w3U%3D&reserved=0
> >> > >
> >> >
> >> > tar -zxvf met-9.1.1.20201118.tar.gz
> >> >
> >> > cd met-9.1.1
> >> >
> >> > export CXX=icpc
> >> >
> >> > export F77=ifort
> >> >
> >> > export CC=icc
> >> >
> >> > export MET_NETCDF=/raid-11/LS/evans36/software/netcdf
> >> >
> >> > export MET_HDF5=/raid-11/LS/evans36/software/hdf5
> >> >
> >> > export MET_BUFRLIB=/raid-11/LS/evans36/software/bufrlib
> >> >
> >> > export MET_GSL=/raid-11/LS/evans36/software/gsl
> >> >
> >> > export
> MET_GRIB2CINC=/raid-11/LS/evans36/software/grib2-new/g2clib-1.6.0
> >> >
> >> > export
> MET_GRIB2CLIB=/raid-11/LS/evans36/software/grib2-new/g2clib-1.6.0
> >> >
> >> > export CFLAGS="-D__64BIT__"
> >> >
> >> > ./configure --prefix=/raid-08/LS/spence98/met-9.1.1 --enable-
grib2
> >> >
> >> > make
> >> >
> >> > make check
> >> >
> >> > make install
> >> >
> >> > Thanks for your help!
> >> >
> >> > Michelle
> >> > ________________________________
> >> > From: John Halley Gotway via RT <met_help at ucar.edu>
> >> > Sent: Wednesday, December 30, 2020 12:56 PM
> >> > To: Michelle Rose Spencer <spence98 at uwm.edu>
> >> > Subject: Re: [rt.rap.ucar.edu #98084] MET Error - Out of memory
> reading
> >> > grib2 data
> >> >
> >> > Hi Michelle,
> >> >
> >> > I see you're having trouble running MET on GRIB2 data. And I
think
> that
> >> > error message is pointing you to the most likely culprit:
> >> >
> >> >
> >> > *ERROR : Check that MET and the GRIB2C library were compiled
> >> consistently,
> >> > either with or without the -D__64BIT__ flag.*
> >> >
> >> > Every time this runtime error has occurred with GRIB2 in the
past,
> it's
> >> > been due to this problem in how the code was compiled. Do you
know who
> >> > compiled it?
> >> > They will need to rerun the ./configure command either with or
without
> >> the
> >> > -D__64BIT__ flag and rerun make install.
> >> >
> >> > Here's where it's mentioned in the docs:
> >> >
> >> >
> >>
>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdtcenter.github.io%2FMET%2Fdevelop%2FUsers_Guide%2Finstallation.html%3Fhighlight%3D64bit&data=04%7C01%7Cspence98%40uwm.edu%7C488c475c870d46ff8b1c08d8b35d59e4%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637456560832354631%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=oXzdccWx1I81OyQQ7cDbVxyJUCjy0tfq5XrtDxWQL0o%3D&reserved=0
> >> >
> >> > Sorry for this nuisance. I wish the MET configuration step
could be
> >> > enhanced to automatically handle this situation instead of
wasting
> >> users'
> >> > time trying to figure it out. Let me know how it goes or if any
more
> >> > questions arise.
> >> >
> >> > Thanks,
> >> > John Halley Gotway
> >> >
> >> >
> >> > On Wed, Dec 30, 2020 at 11:33 AM Michelle Rose Spencer via RT <
> >> > met_help at ucar.edu> wrote:
> >> >
> >> > >
> >> > > Wed Dec 30 11:33:12 2020: Request 98084 was acted upon.
> >> > > Transaction: Ticket created by spence98 at uwm.edu
> >> > > Queue: met_help
> >> > > Subject: MET Error - Out of memory reading grib2 data
> >> > > Owner: Nobody
> >> > > Requestors: spence98 at uwm.edu
> >> > > Status: new
> >> > > Ticket <URL:
> >> >
> >>
>
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frt.rap.ucar.edu%2Frt%2FTicket%2FDisplay.html%3Fid%3D98084&data=04%7C01%7Cspence98%40uwm.edu%7C488c475c870d46ff8b1c08d8b35d59e4%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637456560832354631%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=szBYOSxGhYJRXJGtvXYf0JsrMKuaImw0HE1AIFmlhkk%3D&reserved=0
> >> > >
> >> > >
> >> > >
> >> > > Hello,
> >> > >
> >> > > My name is Michelle, and I am trying to use the MET software
but am
> >> > > running into a memory error and am not sure why or how to fix
it. I
> >> have
> >> > > tried using the plot_data_plane tool and MODE, but both are
giving
> me
> >> the
> >> > > same issue. I am using the supercomputer here at my
university, so
> >> memory
> >> > > shouldn't be an issue, so I was wondering if this has been an
issue
> >> for
> >> > > others and if so, what I can do to fix it? I was originally
trying
> to
> >> use
> >> > > NetCDF files, but was having trouble with those, so I created
grib
> >> files
> >> > > from my wrf output instead. I have double checked to ensure
my MET
> and
> >> > > GRIB2C libraries were compiled consistently, so I know that
isn't
> the
> >> > > issue. Any help or guidance would be greatly appreciated!
> >> > >
> >> > >
> >> > > (base) [spence98 at compute-004 ~]$ mode
> >> > > /home/spence98/spence98/13oct14/control_uh.grb2
> >> > > /home/spence98/spence98/13oct14/control_uh.grb2
> >> > > /home/spence98/spence98/13oct14/control_config -outdir
> >> > > /home/spence98/spence98/13oct14/
> >> > >
> >> > > DEBUG 1: Default Config File:
> >> > > /raid-08/LS/spence98/met-
9.1.1/share/met/config/MODEConfig_default
> >> > >
> >> > > DEBUG 1: Match Config File:
> >> > /home/spence98/spence98/13oct14/control_config
> >> > >
> >> > > DEBUG 1: Merge Config File:
> >> > /home/spence98/spence98/13oct14/control_config
> >> > >
> >> > > ERROR :
> >> > >
> >> > > ERROR : Out of memory reading GRIB2 data! Exiting!
> >> > >
> >> > > ERROR : Check that MET and the GRIB2C library were compiled
> >> > consistently,
> >> > > either with or without the -D__64BIT__ flag.
> >> > >
> >> > > ERROR :
> >> > >
> >> > > Thank you,
> >> > >
> >> > > Michelle Spencer
> >> > > Graduate Research Assistant
> >> > > Atmospheric Science Program
> >> > > University of Wisconsin-Milwaukee
> >> > >
> >> > >
> >> > >
> >> >
> >> >
> >> >
> >>
> >>
> >>
>
>
>
------------------------------------------------
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