[ncl-install] Installing NCL 6.2.1 on CentOS 6.5 with GCC 4.4.7
Mary Haley
haley at ucar.edu
Sat Oct 18 10:03:14 MDT 2014
What exactly are you typing that causes this error message? That is, do
you get this error no matter what NCL script you try to execute, or only
when you try to use ncl_convert2nc?
Do you get a similar error when you type:
ng4ex xy01n -clean
? This command should run a sample NCL script called "xy01n.ncl", which
will cause an X11 window with an XY plot to pop up. You'll need to click on
this with your left mouse button for it to go away.
If the problem seems to be limited to ncl_convert2nc, then the issue is
likely with the GRIB file, and it would help if we could have this file so
we can test it here.
Thanks,
--Mary
On Fri, Oct 17, 2014 at 11:40 AM, David, Cedric H (329C) <
Cedric.David at jpl.nasa.gov> wrote:
> Dear all,
> I am attempting to install NCL 6.2.1 on CentOS 6.5 and I am having some
> difficulties. I am guessing my issue may be related to not having the same
> CentOS as that of the binary files available on
> https://www.earthsystemgrid.org/ but I have limited freedom on the
> operating system. The computer I am using is a virtual machine deployed on
> the Microsoft Azure Cloud. My choice of which version of CentOS is limited
> to 6.5 or 7. The last time I tried to install NCL was on a different
> machine with exact match on the available binaries (CentOS 5.10, x86_64,
> GCC 4.1.2, NCL 6.2.0) and had no problem. The program I’m attempting to
> run converts part of a grib file into an netcdf file.
> I have read through the following:
> http://www.ncl.ucar.edu/Download/
> http://www.ncl.ucar.edu/Download/linux.shtml
> I have tried looking for previous posts on (but I just get 404 errors):
> http://www.ncl.ucar.edu/Support/posting_guidelines.shtml
> So I still can’t figure it out. If someone on this list could help, I’d
> very much appreciate it! Disclaimer, I am new to administrating my own
> Linux machine…
> My issue is summarized below,
> Thanks much!
> Cedric
>
>
> My machine is a CentOS 6.5, 64 bits, with GCC 447:
>
> [chdavid at flashflood process]$ uname -m
>
> x86_64
>
> [chdavid at flashflood process]$
>
> [chdavid at flashflood process]$ cat /etc/issue
>
> CentOS release 6.5 (Final)
>
> Kernel \r on an \m
>
>
> [chdavid at flashflood process]$
>
> [chdavid at flashflood process]$ gcc --version
>
> gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
>
> Copyright (C) 2010 Free Software Foundation, Inc.
>
> This is free software; see the source for copying conditions. There is NO
>
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
>
>
> [chdavid at flashflood process]$
>
> I have tried several binaries, one at a time:
>
> [chdavid at flashflood ncl-6.2.1]$ ls ../ncl_ncarg-6.2.*.Linux*
>
> ../ncl_ncarg-6.2.0.Linux_RHEL5.10_x86_64_nodap_gcc412.tar.gz
> ../ncl_ncarg-6.2.1.Linux_RHEL6.4_x86_64_nodap_gcc447.tar.gz
>
> ../ncl_ncarg-6.2.0.Linux_RHEL6.2_x86_64_nodap_gcc472.tar.gz
> ../ncl_ncarg-6.2.1.Linux_RHEL6.4_x86_64_nodap_gcc472.tar.gz
>
> ../ncl_ncarg-6.2.1.Linux_RHEL5.10_x86_64_nodap_gcc412.tar.gz
> ../ncl_ncarg-6.2.1.Linux_SL6.5_x86_64_gcc447.tar.gz
>
> ../ncl_ncarg-6.2.1.Linux_RHEL6.4_x86_64_gcc472.tar.gz
> ../ncl_ncarg-6.2.1.Linux_SL6.5_x86_64_nodap_gcc447.tar.gz
>
> every time I had NCL installed in ~/installz/ncl-6.2.1/ and the
> environment variables set:
>
> [chdavid at flashflood process]$ echo $NCARG_ROOT
>
> /home/chdavid/installz/ncl-6.2.1
>
> [chdavid at flashflood process]$
>
> [chdavid at flashflood process]$ which ncl
>
> ~/installz/ncl-6.2.1/bin/ncl
>
> [chdavid at flashflood process]$
>
> [chdavid at flashflood process]$
>
> If I use one of the binaries with a version of GCC equal or earlier to
> mine, I get:
> *** glibc detected *** ncl: corrupted double-linked list:
> 0x00000000080a5600 ***
>
> ======= Backtrace: =========
>
> /lib64/libc.so.6[0x383bc75e76]
>
> /lib64/libc.so.6[0x383bc762fd]
>
> /lib64/libc.so.6[0x383bc79125]
>
> /lib64/libc.so.6(__libc_malloc+0x71)[0x383bc7a6b1]
>
> ncl(NclMalloc+0x10)[0x717654]
>
> ncl(_NclGribVersion+0x39)[0x6f3809]
>
> ncl(_NclFileCreate+0x17f)[0x72c8f0]
>
> ncl(_NclCreateFile+0x410)[0x6f3796]
>
> ncl(_NclIAddFile+0x1c4)[0x803467]
>
> ncl(CallINTRINSIC_FUNC_CALL+0x43)[0x7cb1ba]
>
> ncl(_NclExecute+0x3db)[0x7d2ca5]
>
> ncl(yyparse+0x78f)[0x69a409]
>
> ncl(NclDriver+0xc36)[0x696b55]
>
> ncl(main+0x9)[0x6931d1]
>
> /lib64/libc.so.6(__libc_start_main+0xfd)[0x383bc1ed5d]
>
> ncl(vfprintf+0x589)[0x693119]
>
> ======= Memory map: ========
>
> 00400000-02364000 r-xp 00000000 08:01 1709097
> /home/chdavid/installz/ncl-6.2.1/bin/ncl
>
> 02563000-027a0000 rw-p 01f63000 08:01 1709097
> /home/chdavid/installz/ncl-6.2.1/bin/ncl
>
> 027a0000-039e0000 rw-p 00000000 00:00 0
>
> 04808000-08148000 rw-p 00000000 00:00 0
> [heap]
>
> 383b800000-383b820000 r-xp 00000000 08:01 1321949
> /lib64/ld-2.12.so
>
> 383ba1f000-383ba20000 r--p 0001f000 08:01 1321949
> /lib64/ld-2.12.so
>
> 383ba20000-383ba21000 rw-p 00020000 08:01 1321949
> /lib64/ld-2.12.so
>
> 383ba21000-383ba22000 rw-p 00000000 00:00 0
>
> 383bc00000-383bd8a000 r-xp 00000000 08:01 1321952
> /lib64/libc-2.12.so
>
> 383bd8a000-383bf8a000 ---p 0018a000 08:01 1321952
> /lib64/libc-2.12.so
>
> 383bf8a000-383bf8e000 r--p 0018a000 08:01 1321952
> /lib64/libc-2.12.so
>
> 383bf8e000-383bf8f000 rw-p 0018e000 08:01 1321952
> /lib64/libc-2.12.so
>
> 383bf8f000-383bf94000 rw-p 00000000 00:00 0
>
> 383c000000-383c017000 r-xp 00000000 08:01 1321953
> /lib64/libpthread-2.12.so
>
> 383c017000-383c217000 ---p 00017000 08:01 1321953
> /lib64/libpthread-2.12.so
>
> 383c217000-383c218000 r--p 00017000 08:01 1321953
> /lib64/libpthread-2.12.so
>
> 383c218000-383c219000 rw-p 00018000 08:01 1321953
> /lib64/libpthread-2.12.so
>
> 383c219000-383c21d000 rw-p 00000000 00:00 0
>
> 383c400000-383c402000 r-xp 00000000 08:01 1321962
> /lib64/libdl-2.12.so
>
> 383c402000-383c602000 ---p 00002000 08:01 1321962
> /lib64/libdl-2.12.so
>
> 383c602000-383c603000 r--p 00002000 08:01 1321962
> /lib64/libdl-2.12.so
>
> 383c603000-383c604000 rw-p 00003000 08:01 1321962
> /lib64/libdl-2.12.so
>
> 383cc00000-383cc07000 r-xp 00000000 08:01 1321958
> /lib64/librt-2.12.so
>
> 383cc07000-383ce06000 ---p 00007000 08:01 1321958
> /lib64/librt-2.12.so
>
> 383ce06000-383ce07000 r--p 00006000 08:01 1321958
> /lib64/librt-2.12.so
>
> 383ce07000-383ce08000 rw-p 00007000 08:01 1321958
> /lib64/librt-2.12.so
>
> 383d000000-383d083000 r-xp 00000000 08:01 1321955
> /lib64/libm-2.12.so
>
> 383d083000-383d282000 ---p 00083000 08:01 1321955
> /lib64/libm-2.12.so
>
> 383d282000-383d283000 r--p 00082000 08:01 1321955
> /lib64/libm-2.12.so
>
> 383d283000-383d284000 rw-p 00083000 08:01 1321955
> /lib64/libm-2.12.so
>
> 383ec00000-383ec16000 r-xp 00000000 08:01 1321956
> /lib64/libgcc_s-4.4.7-20120601.so.1
>
> 383ec16000-383ee15000 ---p 00016000 08:01 1321956
> /lib64/libgcc_s-4.4.7-20120601.so.1
>
> 383ee15000-383ee16000 rw-p 00015000 08:01 1321956
> /lib64/libgcc_s-4.4.7-20120601.so.1
>
> 383f000000-383f0e8000 r-xp 00000000 08:01 791378
> /usr/lib64/libstdc++.so.6.0.13
>
> 383f0e8000-383f2e8000 ---p 000e8000 08:01 791378
> /usr/lib64/libstdc++.so.6.0.13
>
> 383f2e8000-383f2ef000 r--p 000e8000 08:01 791378
> /usr/lib64/libstdc++.so.6.0.13
>
> 383f2ef000-383f2f1000 rw-p 000ef000 08:01 791378
> /usr/lib64/libstdc++.so.6.0.13
>
> 383f2f1000-383f306000 rw-p 00000000 00:00 0
>
> 383f800000-383f898000 r-xp 00000000 08:01 787710
> /usr/lib64/libfreetype.so.6.3.22
>
> 383f898000-383fa97000 ---p 00098000 08:01 787710
> /usr/lib64/libfreetype.so.6.3.22
>
> 383fa97000-383fa9d000 rw-p 00097000 08:01 787710
> /usr/lib64/libfreetype.so.6.3.22
>
> 383fc00000-383fc34000 r-xp 00000000 08:01 785923
> /usr/lib64/libfontconfig.so.1.4.4
>
> 383fc34000-383fe34000 ---p 00034000 08:01 785923
> /usr/lib64/libfontconfig.so.1.4.4
>
> 383fe34000-383fe36000 rw-p 00034000 08:01 785923
> /usr/lib64/libfontconfig.so.1.4.4
>
> 3840400000-3840537000 r-xp 00000000 08:01 786097
> /usr/lib64/libX11.so.6.3.0
>
> 3840537000-3840737000 ---p 00137000 08:01 786097
> /usr/lib64/libX11.so.6.3.0
>
> 3840737000-384073d000 rw-p 00137000 08:01 786097
> /usr/lib64/libX11.so.6.3.0
>
> 3841000000-384101d000 r-xp 00000000 08:01 786000
> /usr/lib64/libxcb.so.1.1.0
>
> 384101d000-384121d000 ---p 0001d000 08:01 786000
> /usr/lib64/libxcb.so.1.1.0
>
> 384121d000-384121e000 rw-p 0001d000 08:01 786000
> /usr/lib64/libxcb.so.1.1.0
>
> 3841400000-3841426000 r-xp 00000000 08:01 1318702
> /lib64/libexpat.so.1.5.2
>
> 3841426000-3841625000 ---p 00026000 08:01 1318702
> /lib64/libexpat.so.1.5.2
>
> 3841625000-3841628000 rw-p 00025000 08:01 1318702
> /lib64/libexpat.so.1.5.2
>
> 3843800000-3843810000 r-xp 00000000 08:01 1308283
> /lib64/libbz2.so.1.0.4
>
> 3843810000-3843a0f000 ---p 00010000 08:01 1308283
> /lib64/libbz2.so.1.0.4
>
> 3843a0f000-3843a11000 rw-p 0000f000 08:01 1308283
> /lib64/libbz2.so.1.0.4
>
> 3844000000-3844012000 r-xp 00000000 08:01 786098
> /usr/lib64/libXext.so.6.4.0
>
> 3844012000-3844212000 ---p 00012000 08:01 786098
> /usr/lib64/libXext.so.6.4.0
>
> 3844212000-3844213000 rw-p 00012000 08:01 786098
> /usr/lib64/libXext.so.6.4.0
>
> 3844800000-3844802000 r-xp 00000000 08:01 798978
> /usr/lib64/libXau.so.6.0.0
>
> 3844802000-3844a02000 ---p 00002000 08:01 798978
> /usr/lib64/libXau.so.6.0.0
>
> 3844a02000-3844a03000 rw-p 00002000 08:01 798978
> /usr/lib64/libXau.so.6.0.0
>
> 3844c00000-3844c09000 r-xp 00000000 08:01 786099
> /usr/lib64/libXrender.so.1.3.0
>
> 3844c09000-3844e09000 ---p 00009000 08:01 786099
> /usr/lib64/libXrender.so.1.3.0
>
> 3844e09000-3844e0a000 rw-p 00009000 08:01 786099
> /usr/lib64/libXrender.so.1.3.0
>
> 7fd2c37a3000-7fd2c38ad000 rw-p 00000000 00:00 0 Aborted (core dumped)
>
> If I use a version of GCC that’s more recent than mine, I get:
>
> ncl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found
> (required by ncl)
>
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