[Met_help] [rt.rap.ucar.edu #91161] History for rpl_malloc or problem with the configure
David Fillmore via RT
met_help at ucar.edu
Tue Jul 23 10:33:14 MDT 2019
----------------------------------------------------------------
Initial Request
----------------------------------------------------------------
All,
I'm trying to compile met-8.1.1 on a computer using Intel compilers. When I
first configured the system, I received an error:
checking for suffix of executables...
checking whether we are cross compiling... configure: error: in
`/gpfs/home/tyndalld/met-8.1.1':
configure: error: cannot run C++ compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details
I looked at the configure script and excluded this particular check by
setting cross_compiling from no to yes. Now, this may have broken other
things, as I now get an error message when compiling:
/opt/intel/composer_xe_2011_sp1.6.233/bin/intel64/icc -DHAVE_CONFIG_H -I.
-I../../.. -I../../../src/basic/vx_cal -fPIC -I../../../src/basic/vx_config
-I../../../src/basic/vx_log -I../../../src/basic/vx_math
-I../../../src/basic/vx_util -I../../../src/libcode/vx_afm
-I../../../src/libcode/vx_analysis_util -I../../../src/libcode/vx_color
-I../../../src/libcode/vx_data2d -I../../../src/libcode/vx_data2d_factory
-I../../../src/libcode/vx_data2d_grib -I../../../src/libcode/vx_data2d_grib2
-I../../../src/libcode/vx_data2d_nccf
-I../../../src/libcode/vx_data2d_nc_met
-I../../../src/libcode/vx_data2d_nc_pinterp
-I../../../src/libcode/vx_data2d_python
-I../../../src/libcode/vx_python_utils -I../../../src/libcode/vx_geodesy
-I../../../src/libcode/vx_gis -I../../../src/libcode/vx_gnomon
-I../../../src/libcode/vx_grid -I../../../src/libcode/vx_gsl_prob
-I../../../src/libcode/vx_nav -I../../../src/libcode/vx_nc_obs
-I../../../src/libcode/vx_nc_util -I../../../src/libcode/vx_pb_util
-I../../../src/libcode/vx_plot_util -I../../../src/libcode/vx_ps
-I../../../src/libcode/vx_pxm -I../../../src/libcode/vx_render
-I../../../src/libcode/vx_regrid -I../../../src/libcode/vx_shapedata
-I../../../src/libcode/vx_solar -I../../../src/libcode/vx_statistics
-I../../../src/libcode/vx_stat_out -I../../../src/libcode/vx_summary
-I../../../src/libcode/vx_time_series -I../../../src/libcode/vx_tc_util
-I/home/tyndalld/software/netcdf/include
-I/home/tyndalld/software/hdf5/include
-I/home/tyndalld/software/g2clib-1.6.0
-I/home/tyndalld/miniconda3/envs/python27/include/python2.7
-I/home/tyndalld/software/gsl/include
-I/home/tyndalld/software/cairo/include
-I/home/tyndalld/software/freetype/include -DBLOCK4 -DWITH_GRIB2
-DWITH_PYTHON -DMET_BASE="\"/home/tyndalld/met/share/met\"" -g -MT
libvx_color_a-color_parser_yacc.o -MD -MP -MF
.deps/libvx_color_a-color_parser_yacc.Tpo -c -o
libvx_color_a-color_parser_yacc.o `test -f 'color_parser_yacc.cc' || echo
'./'`color_parser_yacc.cc
../../../src/basic/vx_config/threshold.h(82): warning #411: class
"PercThreshInfo" defines no constructor to initialize the following:
const member "PercThreshInfo::type"
const member "PercThreshInfo::short_name"
const member "PercThreshInfo::short_name_length"
const member "PercThreshInfo::long_name"
struct PercThreshInfo {
^
color_parser_yacc.cc(1255): error: identifier "rpl_malloc" is undefined
(union yyalloc *) YYSTACK_ALLOC (YYSTACK_BYTES (yystacksize));
^
compilation aborted for color_parser_yacc.cc (code 2)
make[4]: *** [libvx_color_a-color_parser_yacc.o] Error 2
make[4]: Leaving directory
`/gpfs/home/tyndalld/met-8.1.1/src/libcode/vx_color'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/gpfs/home/tyndalld/met-8.1.1/src/libcode'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/gpfs/home/tyndalld/met-8.1.1/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/gpfs/home/tyndalld/met-8.1.1'
make: *** [all] Error 2
Can anyone help me with what I'm missing here? I'm not sure if my earlier
hack has broken my build or not (and if so, what's the proper way of solving
my earlier problem)? Thanks,
-Dan
Dr. Daniel P. Tyndall
United States Naval Research Laboratory
7 Grace Hopper Avenue Stop #2
Monterey, CA 93943
Phone: (831) 656-4054 - Fax: (831) 656-4769 - Cell: (630) 440-8622
Email: <mailto:dan.tyndall at nrlmry.navy.mil> dan.tyndall at nrlmry.navy.mil
After hours email: <mailto:dan.tyndall at outlook.com> dan.tyndall at outlook.com
----------------------------------------------------------------
Complete Ticket History
----------------------------------------------------------------
Subject: rpl_malloc or problem with the configure
From: David Fillmore
Time: Fri Jul 19 13:59:14 2019
Hi Dan -
I just saw this same error on an Ubuntu instance building with gcc
7.3,
so it is not specific to the Intel compilers.
As a temporary fix, I was able to complete the build by editing the
config.h file
in the top level met directory.
I commented out the lines:
#define malloc rpl_malloc
#define realloc rpl_realloc
On my system, I also needed to comment out:
#defiine size_t unsigned int
on my system.
We are working on a bugfix and will update the 8.1 version as soon as
resolved.
Let me know if the config.h changes help...
thanks,
David
On Fri, Jul 19, 2019 at 1:46 PM Tyndall, Dr. Dan via RT
<met_help at ucar.edu>
wrote:
>
> Fri Jul 19 13:46:43 2019: Request 91161 was acted upon.
> Transaction: Ticket created by Dan.Tyndall at nrlmry.navy.mil
> Queue: met_help
> Subject: rpl_malloc or problem with the configure
> Owner: Nobody
> Requestors: Dan.Tyndall at nrlmry.navy.mil
> Status: new
> Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=91161 >
>
>
> All,
>
>
>
> I'm trying to compile met-8.1.1 on a computer using Intel compilers.
When I
> first configured the system, I received an error:
>
>
>
> checking for suffix of executables...
>
> checking whether we are cross compiling... configure: error: in
> `/gpfs/home/tyndalld/met-8.1.1':
>
> configure: error: cannot run C++ compiled programs.
>
> If you meant to cross compile, use `--host'.
>
> See `config.log' for more details
>
>
>
> I looked at the configure script and excluded this particular check
by
> setting cross_compiling from no to yes. Now, this may have broken
other
> things, as I now get an error message when compiling:
>
>
>
> /opt/intel/composer_xe_2011_sp1.6.233/bin/intel64/icc
-DHAVE_CONFIG_H -I.
> -I../../.. -I../../../src/basic/vx_cal -fPIC
> -I../../../src/basic/vx_config
> -I../../../src/basic/vx_log -I../../../src/basic/vx_math
> -I../../../src/basic/vx_util -I../../../src/libcode/vx_afm
> -I../../../src/libcode/vx_analysis_util
-I../../../src/libcode/vx_color
> -I../../../src/libcode/vx_data2d
-I../../../src/libcode/vx_data2d_factory
> -I../../../src/libcode/vx_data2d_grib
> -I../../../src/libcode/vx_data2d_grib2
> -I../../../src/libcode/vx_data2d_nccf
> -I../../../src/libcode/vx_data2d_nc_met
> -I../../../src/libcode/vx_data2d_nc_pinterp
> -I../../../src/libcode/vx_data2d_python
> -I../../../src/libcode/vx_python_utils
-I../../../src/libcode/vx_geodesy
> -I../../../src/libcode/vx_gis -I../../../src/libcode/vx_gnomon
> -I../../../src/libcode/vx_grid -I../../../src/libcode/vx_gsl_prob
> -I../../../src/libcode/vx_nav -I../../../src/libcode/vx_nc_obs
> -I../../../src/libcode/vx_nc_util -I../../../src/libcode/vx_pb_util
> -I../../../src/libcode/vx_plot_util -I../../../src/libcode/vx_ps
> -I../../../src/libcode/vx_pxm -I../../../src/libcode/vx_render
> -I../../../src/libcode/vx_regrid -I../../../src/libcode/vx_shapedata
> -I../../../src/libcode/vx_solar -I../../../src/libcode/vx_statistics
> -I../../../src/libcode/vx_stat_out -I../../../src/libcode/vx_summary
> -I../../../src/libcode/vx_time_series
-I../../../src/libcode/vx_tc_util
> -I/home/tyndalld/software/netcdf/include
> -I/home/tyndalld/software/hdf5/include
> -I/home/tyndalld/software/g2clib-1.6.0
> -I/home/tyndalld/miniconda3/envs/python27/include/python2.7
> -I/home/tyndalld/software/gsl/include
> -I/home/tyndalld/software/cairo/include
> -I/home/tyndalld/software/freetype/include -DBLOCK4 -DWITH_GRIB2
> -DWITH_PYTHON -DMET_BASE="\"/home/tyndalld/met/share/met\"" -g -MT
> libvx_color_a-color_parser_yacc.o -MD -MP -MF
> .deps/libvx_color_a-color_parser_yacc.Tpo -c -o
> libvx_color_a-color_parser_yacc.o `test -f 'color_parser_yacc.cc' ||
echo
> './'`color_parser_yacc.cc
>
> ../../../src/basic/vx_config/threshold.h(82): warning #411: class
> "PercThreshInfo" defines no constructor to initialize the following:
>
> const member "PercThreshInfo::type"
>
> const member "PercThreshInfo::short_name"
>
> const member "PercThreshInfo::short_name_length"
>
> const member "PercThreshInfo::long_name"
>
> struct PercThreshInfo {
>
> ^
>
>
>
> color_parser_yacc.cc(1255): error: identifier "rpl_malloc" is
undefined
>
> (union yyalloc *) YYSTACK_ALLOC (YYSTACK_BYTES
(yystacksize));
>
> ^
>
>
>
> compilation aborted for color_parser_yacc.cc (code 2)
>
> make[4]: *** [libvx_color_a-color_parser_yacc.o] Error 2
>
> make[4]: Leaving directory
> `/gpfs/home/tyndalld/met-8.1.1/src/libcode/vx_color'
>
> make[3]: *** [all-recursive] Error 1
>
> make[3]: Leaving directory `/gpfs/home/tyndalld/met-
8.1.1/src/libcode'
>
> make[2]: *** [all-recursive] Error 1
>
> make[2]: Leaving directory `/gpfs/home/tyndalld/met-8.1.1/src'
>
> make[1]: *** [all-recursive] Error 1
>
> make[1]: Leaving directory `/gpfs/home/tyndalld/met-8.1.1'
>
> make: *** [all] Error 2
>
>
>
> Can anyone help me with what I'm missing here? I'm not sure if my
earlier
> hack has broken my build or not (and if so, what's the proper way of
> solving
> my earlier problem)? Thanks,
>
>
>
> -Dan
>
>
>
> Dr. Daniel P. Tyndall
>
> United States Naval Research Laboratory
>
> 7 Grace Hopper Avenue Stop #2
>
> Monterey, CA 93943
>
> Phone: (831) 656-4054 - Fax: (831) 656-4769 - Cell: (630) 440-8622
>
> Email: <mailto:dan.tyndall at nrlmry.navy.mil>
dan.tyndall at nrlmry.navy.mil
>
> After hours email: <mailto:dan.tyndall at outlook.com>
> dan.tyndall at outlook.com
>
>
>
>
>
------------------------------------------------
Subject: rpl_malloc or problem with the configure
From: Tyndall, Dr. Dan
Time: Fri Jul 19 21:01:28 2019
Hi David,
Thank you for the help! I also needed to export F77 to the location of
my
ifort, as well as set the cross_compiling flag to yes (as I mentioned
below,
even though I'm not cross-compiling). I now have everything
compiled... I
think I will test next week though.
-Dan
-----Original Message-----
From: David Fillmore via RT [mailto:met_help at ucar.edu]
Sent: Friday, July 19, 2019 12:59 PM
To: Tyndall, Dr. Dan
Cc: met_help at mailman.ucar.edu
Subject: Re: [rt.rap.ucar.edu #91161] rpl_malloc or problem with the
configure
Hi Dan -
I just saw this same error on an Ubuntu instance building with gcc
7.3,
so it is not specific to the Intel compilers.
As a temporary fix, I was able to complete the build by editing the
config.h file
in the top level met directory.
I commented out the lines:
#define malloc rpl_malloc
#define realloc rpl_realloc
On my system, I also needed to comment out:
#defiine size_t unsigned int
on my system.
We are working on a bugfix and will update the 8.1 version as soon as
resolved.
Let me know if the config.h changes help...
thanks,
David
On Fri, Jul 19, 2019 at 1:46 PM Tyndall, Dr. Dan via RT
<met_help at ucar.edu>
wrote:
>
> Fri Jul 19 13:46:43 2019: Request 91161 was acted upon.
> Transaction: Ticket created by Dan.Tyndall at nrlmry.navy.mil
> Queue: met_help
> Subject: rpl_malloc or problem with the configure
> Owner: Nobody
> Requestors: Dan.Tyndall at nrlmry.navy.mil
> Status: new
> Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=91161 >
>
>
> All,
>
>
>
> I'm trying to compile met-8.1.1 on a computer using Intel compilers.
When I
> first configured the system, I received an error:
>
>
>
> checking for suffix of executables...
>
> checking whether we are cross compiling... configure: error: in
> `/gpfs/home/tyndalld/met-8.1.1':
>
> configure: error: cannot run C++ compiled programs.
>
> If you meant to cross compile, use `--host'.
>
> See `config.log' for more details
>
>
>
> I looked at the configure script and excluded this particular check
by
> setting cross_compiling from no to yes. Now, this may have broken
other
> things, as I now get an error message when compiling:
>
>
>
> /opt/intel/composer_xe_2011_sp1.6.233/bin/intel64/icc
-DHAVE_CONFIG_H -I.
> -I../../.. -I../../../src/basic/vx_cal -fPIC
> -I../../../src/basic/vx_config
> -I../../../src/basic/vx_log -I../../../src/basic/vx_math
> -I../../../src/basic/vx_util -I../../../src/libcode/vx_afm
> -I../../../src/libcode/vx_analysis_util
-I../../../src/libcode/vx_color
> -I../../../src/libcode/vx_data2d
-I../../../src/libcode/vx_data2d_factory
> -I../../../src/libcode/vx_data2d_grib
> -I../../../src/libcode/vx_data2d_grib2
> -I../../../src/libcode/vx_data2d_nccf
> -I../../../src/libcode/vx_data2d_nc_met
> -I../../../src/libcode/vx_data2d_nc_pinterp
> -I../../../src/libcode/vx_data2d_python
> -I../../../src/libcode/vx_python_utils
-I../../../src/libcode/vx_geodesy
> -I../../../src/libcode/vx_gis -I../../../src/libcode/vx_gnomon
> -I../../../src/libcode/vx_grid -I../../../src/libcode/vx_gsl_prob
> -I../../../src/libcode/vx_nav -I../../../src/libcode/vx_nc_obs
> -I../../../src/libcode/vx_nc_util -I../../../src/libcode/vx_pb_util
> -I../../../src/libcode/vx_plot_util -I../../../src/libcode/vx_ps
> -I../../../src/libcode/vx_pxm -I../../../src/libcode/vx_render
> -I../../../src/libcode/vx_regrid -I../../../src/libcode/vx_shapedata
> -I../../../src/libcode/vx_solar -I../../../src/libcode/vx_statistics
> -I../../../src/libcode/vx_stat_out -I../../../src/libcode/vx_summary
> -I../../../src/libcode/vx_time_series
-I../../../src/libcode/vx_tc_util
> -I/home/tyndalld/software/netcdf/include
> -I/home/tyndalld/software/hdf5/include
> -I/home/tyndalld/software/g2clib-1.6.0
> -I/home/tyndalld/miniconda3/envs/python27/include/python2.7
> -I/home/tyndalld/software/gsl/include
> -I/home/tyndalld/software/cairo/include
> -I/home/tyndalld/software/freetype/include -DBLOCK4 -DWITH_GRIB2
> -DWITH_PYTHON -DMET_BASE="\"/home/tyndalld/met/share/met\"" -g -MT
> libvx_color_a-color_parser_yacc.o -MD -MP -MF
> .deps/libvx_color_a-color_parser_yacc.Tpo -c -o
> libvx_color_a-color_parser_yacc.o `test -f 'color_parser_yacc.cc' ||
echo
> './'`color_parser_yacc.cc
>
> ../../../src/basic/vx_config/threshold.h(82): warning #411: class
> "PercThreshInfo" defines no constructor to initialize the following:
>
> const member "PercThreshInfo::type"
>
> const member "PercThreshInfo::short_name"
>
> const member "PercThreshInfo::short_name_length"
>
> const member "PercThreshInfo::long_name"
>
> struct PercThreshInfo {
>
> ^
>
>
>
> color_parser_yacc.cc(1255): error: identifier "rpl_malloc" is
undefined
>
> (union yyalloc *) YYSTACK_ALLOC (YYSTACK_BYTES
(yystacksize));
>
> ^
>
>
>
> compilation aborted for color_parser_yacc.cc (code 2)
>
> make[4]: *** [libvx_color_a-color_parser_yacc.o] Error 2
>
> make[4]: Leaving directory
> `/gpfs/home/tyndalld/met-8.1.1/src/libcode/vx_color'
>
> make[3]: *** [all-recursive] Error 1
>
> make[3]: Leaving directory `/gpfs/home/tyndalld/met-
8.1.1/src/libcode'
>
> make[2]: *** [all-recursive] Error 1
>
> make[2]: Leaving directory `/gpfs/home/tyndalld/met-8.1.1/src'
>
> make[1]: *** [all-recursive] Error 1
>
> make[1]: Leaving directory `/gpfs/home/tyndalld/met-8.1.1'
>
> make: *** [all] Error 2
>
>
>
> Can anyone help me with what I'm missing here? I'm not sure if my
earlier
> hack has broken my build or not (and if so, what's the proper way of
> solving
> my earlier problem)? Thanks,
>
>
>
> -Dan
>
>
>
> Dr. Daniel P. Tyndall
>
> United States Naval Research Laboratory
>
> 7 Grace Hopper Avenue Stop #2
>
> Monterey, CA 93943
>
> Phone: (831) 656-4054 - Fax: (831) 656-4769 - Cell: (630) 440-8622
>
> Email: <mailto:dan.tyndall at nrlmry.navy.mil>
dan.tyndall at nrlmry.navy.mil
>
> After hours email: <mailto:dan.tyndall at outlook.com>
> dan.tyndall at outlook.com
>
>
>
>
>
------------------------------------------------
Subject: rpl_malloc or problem with the configure
From: David Fillmore
Time: Tue Jul 23 10:33:12 2019
Dan -
Thanks or the information.
We have created a bugfix issue to resolve this for MET release 8.1.2.
Please let us know if you encounter any further configure/build
issues.
David
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