Hi guys. I'm a fresh new user of Isca. I encounter problems in compiling isca when I run the held_suarez test. The complete error message is copied below in Error output. I guess the main error message is ld: cannot find -lmpifort.
Error output
2021-11-27 13:45:03,511 - isca - WARNING - Environment variable GFDL_SOC not set, but this is only required if using SocratesCodebase. Setting to None
2021-11-27 13:45:03,571 - isca - INFO - RRTM compilation disabled.
2021-11-27 13:45:03,571 - isca - INFO - SOCRATES compilation disabled.
2021-11-27 13:45:03,577 - isca - INFO - Writing path_names to '/scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/build/held_suarez/path_names'
2021-11-27 13:45:03,586 - isca - INFO - Running compiler
2021-11-27 13:45:03,592 - isca - INFO - load modules for isca
2021-11-27 13:45:03,667 - isca - INFO - The following modules were not unloaded:
2021-11-27 13:45:03,667 - isca - INFO - (Use "module --force purge" to unload all):
2021-11-27 13:45:03,667 - isca - INFO - 1) xalt/1.1.2
2021-11-27 13:45:04,058 - isca - INFO - Compiling postprocessing tools
2021-11-27 13:45:04,066 - isca - INFO - load modules for isca
2021-11-27 13:45:04,158 - isca - INFO - The following modules were not unloaded:
2021-11-27 13:45:04,158 - isca - INFO - (Use "module --force purge" to unload all):
2021-11-27 13:45:04,158 - isca - INFO - 1) xalt/1.1.2
2021-11-27 13:45:10,109 - isca - INFO - /home/kong97/.conda/envs/isca_env/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lmpifort
2021-11-27 13:45:10,118 - isca - INFO - ERROR: could not compile combine tool
2021-11-27 13:45:10,124 - isca - INFO - /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/build/held_suarez/path_names
2021-11-27 13:45:10,561 - isca - INFO - ........................................................................................................................... Makefile is ready.
2021-11-27 13:45:10,635 - isca - INFO - mpiifort -Duse_libMPI -Duse_netCDF -Duse_LARGEFILE -DINTERNAL_FILE_NML -DOVERLOAD_C8 -DRRTM_NO_COMPILE -DSOC_NO_COMPILE -I/usr/local/include -I/usr/local/include -fpp -stack_temps -safe_cray_ptr -ftz -assume byterecl -shared-intel -i4 -r8 -g -O2 -diag-disable 6843 -mcmodel large -c /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/code/src/atmos_spectral/init/ic_from_external_file.F90
2021-11-27 13:45:10,717 - isca - INFO - /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/code/src/atmos_spectral/init/ic_from_external_file.F90(34): error #6580: Name in only-list does not exist or is not accessible. [GRID_DOMAIN]
2021-11-27 13:45:10,717 - isca - INFO - trans_spherical_to_grid, grid_domain, spectral_domain, get_grid_domain, &
2021-11-27 13:45:10,717 - isca - INFO - ----------------------------------------------------------^
2021-11-27 13:45:10,717 - isca - INFO - /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/code/src/atmos_spectral/init/ic_from_external_file.F90(34): error #6580: Name in only-list does not exist or is not accessible. [SPECTRAL_DOMAIN]
2021-11-27 13:45:10,717 - isca - INFO - trans_spherical_to_grid, grid_domain, spectral_domain, get_grid_domain, &
2021-11-27 13:45:10,717 - isca - INFO - -----------------------------------------------------------------------^
2021-11-27 13:45:10,722 - isca - INFO - /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/code/src/atmos_spectral/init/ic_from_external_file.F90(124): error #6404: This name does not have a type, and must have an explicit type. [GRID_DOMAIN]
2021-11-27 13:45:10,722 - isca - INFO - call read_data(file_name, u_name, ug, domain=grid_domain)
2021-11-27 13:45:10,722 - isca - INFO - -----------------------------------------------^
2021-11-27 13:45:10,722 - isca - INFO - /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/code/src/atmos_spectral/init/ic_from_external_file.F90(124): error #6285: There is no matching specific subroutine for this generic subroutine call. [READ_DATA]
2021-11-27 13:45:10,722 - isca - INFO - call read_data(file_name, u_name, ug, domain=grid_domain)
2021-11-27 13:45:10,722 - isca - INFO - -----^
2021-11-27 13:45:10,722 - isca - INFO - /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/code/src/atmos_spectral/init/ic_from_external_file.F90(125): error #6285: There is no matching specific subroutine for this generic subroutine call. [READ_DATA]
2021-11-27 13:45:10,722 - isca - INFO - call read_data(file_name, v_name, vg, domain=grid_domain)
2021-11-27 13:45:10,722 - isca - INFO - -----^
2021-11-27 13:45:10,722 - isca - INFO - /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/code/src/atmos_spectral/init/ic_from_external_file.F90(126): error #6285: There is no matching specific subroutine for this generic subroutine call. [READ_DATA]
2021-11-27 13:45:10,722 - isca - INFO - call read_data(file_name, t_name, tg, domain=grid_domain)
2021-11-27 13:45:10,722 - isca - INFO - -----^
2021-11-27 13:45:10,722 - isca - INFO - /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/code/src/atmos_spectral/init/ic_from_external_file.F90(127): error #6285: There is no matching specific subroutine for this generic subroutine call. [READ_DATA]
2021-11-27 13:45:10,722 - isca - INFO - call read_data(file_name, ps_name, psg, domain=grid_domain)
2021-11-27 13:45:10,722 - isca - INFO - -----^
2021-11-27 13:45:10,722 - isca - INFO - /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/code/src/atmos_spectral/init/ic_from_external_file.F90(137): error #6285: There is no matching specific subroutine for this generic subroutine call. [READ_DATA]
2021-11-27 13:45:10,722 - isca - INFO - call read_data(file_name, tr_name, grid_tracers(:,:,:,ntr), domain=grid_domain)
2021-11-27 13:45:10,722 - isca - INFO - -------^
2021-11-27 13:45:10,725 - isca - INFO - compilation aborted for /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/code/src/atmos_spectral/init/ic_from_external_file.F90 (code 1)
2021-11-27 13:45:10,727 - isca - INFO - make: [ic_from_external_file.o] Error 1
2021-11-27 13:45:10,728 - isca - INFO - ERROR: mkmf failed for held_suarez.x
Exception in thread background thread for pid 7309:
Traceback (most recent call last):
File "/home/kong97/.conda/envs/isca_env/lib/python3.9/threading.py", line 973, in _bootstrap_inner
self.run()
File "/home/kong97/.conda/envs/isca_env/lib/python3.9/threading.py", line 910, in run
self._target(self._args, self._kwargs)
File "/home/kong97/.conda/envs/isca_env/lib/python3.9/site-packages/sh.py", line 1662, in wrap
fn(*args, **kwargs)
File "/home/kong97/.conda/envs/isca_env/lib/python3.9/site-packages/sh.py", line 2606, in background_thread
handle_exit_code(exit_code)
File "/home/kong97/.conda/envs/isca_env/lib/python3.9/site-packages/sh.py", line 2304, in fn
return self.command.handle_command_exit_code(exit_code)
File "/home/kong97/.conda/envs/isca_env/lib/python3.9/site-packages/sh.py", line 877, in handle_command_exit_code
raise exc
sh.ErrorReturnCode_1:
STDOUT:
load modules for isca
The following modules were not unloaded:
(Use "module --force purge" to unload all):
1) xalt/1.1.2
Compiling postprocessing tools
load modules for isca
The following modules were not unloaded:
(Use "module --force purge" to unload all):
1) xalt/1.1.2
/home/kong97/.conda/envs/isca_env/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lmpifort
ERROR: could not compile combine tool
cb.compile() # compile the source code to working directory $GFDL_WORK/codebase
File "/home/kong97/Isca/src/extra/python/isca/helpers.py", line 38, in _useworkdir
return fn(*args, *kwargs)
File "/home/kong97/Isca/src/extra/python/isca/helpers.py", line 22, in _destructive
return fn(args, **kwargs)
File "/home/kong97/Isca/src/extra/python/isca/codebase.py", line 279, in compile
for line in sh.bash(P(self.builddir, 'compile.sh'), _iter=True, _err_to_out=True):
File "/home/kong97/.conda/envs/isca_env/lib/python3.9/site-packages/sh.py", line 925, in next
self.wait()
File "/home/kong97/.conda/envs/isca_env/lib/python3.9/site-packages/sh.py", line 849, in wait
self.handle_command_exit_code(exit_code)
File "/home/kong97/.conda/envs/isca_env/lib/python3.9/site-packages/sh.py", line 877, in handle_command_exit_code
raise exc
sh.ErrorReturnCode_1:
STDOUT:
load modules for isca
The following modules were not unloaded:
(Use "module --force purge" to unload all):
1) xalt/1.1.2
Compiling postprocessing tools
load modules for isca
The following modules were not unloaded:
(Use "module --force purge" to unload all):
1) xalt/1.1.2
/home/kong97/.conda/envs/isca_env/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lmpifort
ERROR: could not compile combine tool
I just downloaded Isca yesterday through git clone https://github.com/ExeClim/Isca; the latest commit should be commit 58422936f95bbe310e5cb68849a0f13d9e9c7b06
System Information:
uname_result(system='Linux', node='bell-fe06.rcac.purdue.edu', release='3.10.0-1127.19.1.el7.x86_64', version='#1 SMP Tue Aug 25 17:23:54 UTC 2020', machine='x86_64')
I'm using a cluster at Purdue university. We have both intel and gcc compiler. I tried to use intel compiler. However the previously installed conda and python may be compiled by gcc. Is that a problem? When I follow the install guide of Isca. I load intel compiler first, and then conda install the environment.
I have no clue where the compiling error come from. Any help is appreciated!
Description
Hi guys. I'm a fresh new user of Isca. I encounter problems in compiling isca when I run the held_suarez test. The complete error message is copied below in Error output. I guess the main error message is
ld: cannot find -lmpifort.Error output
2021-11-27 13:45:03,511 - isca - WARNING - Environment variable GFDL_SOC not set, but this is only required if using SocratesCodebase. Setting to None 2021-11-27 13:45:03,571 - isca - INFO - RRTM compilation disabled. 2021-11-27 13:45:03,571 - isca - INFO - SOCRATES compilation disabled. 2021-11-27 13:45:03,577 - isca - INFO - Writing path_names to '/scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/build/held_suarez/path_names' 2021-11-27 13:45:03,586 - isca - INFO - Running compiler 2021-11-27 13:45:03,592 - isca - INFO - load modules for isca 2021-11-27 13:45:03,667 - isca - INFO - The following modules were not unloaded: 2021-11-27 13:45:03,667 - isca - INFO - (Use "module --force purge" to unload all): 2021-11-27 13:45:03,667 - isca - INFO - 1) xalt/1.1.2 2021-11-27 13:45:04,058 - isca - INFO - Compiling postprocessing tools 2021-11-27 13:45:04,066 - isca - INFO - load modules for isca 2021-11-27 13:45:04,158 - isca - INFO - The following modules were not unloaded: 2021-11-27 13:45:04,158 - isca - INFO - (Use "module --force purge" to unload all): 2021-11-27 13:45:04,158 - isca - INFO - 1) xalt/1.1.2 2021-11-27 13:45:10,109 - isca - INFO - /home/kong97/.conda/envs/isca_env/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lmpifort 2021-11-27 13:45:10,118 - isca - INFO - ERROR: could not compile combine tool 2021-11-27 13:45:10,124 - isca - INFO - /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/build/held_suarez/path_names 2021-11-27 13:45:10,561 - isca - INFO - ........................................................................................................................... Makefile is ready. 2021-11-27 13:45:10,635 - isca - INFO - mpiifort -Duse_libMPI -Duse_netCDF -Duse_LARGEFILE -DINTERNAL_FILE_NML -DOVERLOAD_C8 -DRRTM_NO_COMPILE -DSOC_NO_COMPILE -I/usr/local/include -I/usr/local/include -fpp -stack_temps -safe_cray_ptr -ftz -assume byterecl -shared-intel -i4 -r8 -g -O2 -diag-disable 6843 -mcmodel large -c /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/code/src/atmos_spectral/init/ic_from_external_file.F90 2021-11-27 13:45:10,717 - isca - INFO - /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/code/src/atmos_spectral/init/ic_from_external_file.F90(34): error #6580: Name in only-list does not exist or is not accessible. [GRID_DOMAIN] 2021-11-27 13:45:10,717 - isca - INFO - trans_spherical_to_grid, grid_domain, spectral_domain, get_grid_domain, & 2021-11-27 13:45:10,717 - isca - INFO - ----------------------------------------------------------^ 2021-11-27 13:45:10,717 - isca - INFO - /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/code/src/atmos_spectral/init/ic_from_external_file.F90(34): error #6580: Name in only-list does not exist or is not accessible. [SPECTRAL_DOMAIN] 2021-11-27 13:45:10,717 - isca - INFO - trans_spherical_to_grid, grid_domain, spectral_domain, get_grid_domain, & 2021-11-27 13:45:10,717 - isca - INFO - -----------------------------------------------------------------------^ 2021-11-27 13:45:10,722 - isca - INFO - /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/code/src/atmos_spectral/init/ic_from_external_file.F90(124): error #6404: This name does not have a type, and must have an explicit type. [GRID_DOMAIN] 2021-11-27 13:45:10,722 - isca - INFO - call read_data(file_name, u_name, ug, domain=grid_domain) 2021-11-27 13:45:10,722 - isca - INFO - -----------------------------------------------^ 2021-11-27 13:45:10,722 - isca - INFO - /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/code/src/atmos_spectral/init/ic_from_external_file.F90(124): error #6285: There is no matching specific subroutine for this generic subroutine call. [READ_DATA] 2021-11-27 13:45:10,722 - isca - INFO - call read_data(file_name, u_name, ug, domain=grid_domain) 2021-11-27 13:45:10,722 - isca - INFO - -----^ 2021-11-27 13:45:10,722 - isca - INFO - /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/code/src/atmos_spectral/init/ic_from_external_file.F90(125): error #6285: There is no matching specific subroutine for this generic subroutine call. [READ_DATA] 2021-11-27 13:45:10,722 - isca - INFO - call read_data(file_name, v_name, vg, domain=grid_domain) 2021-11-27 13:45:10,722 - isca - INFO - -----^ 2021-11-27 13:45:10,722 - isca - INFO - /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/code/src/atmos_spectral/init/ic_from_external_file.F90(126): error #6285: There is no matching specific subroutine for this generic subroutine call. [READ_DATA] 2021-11-27 13:45:10,722 - isca - INFO - call read_data(file_name, t_name, tg, domain=grid_domain) 2021-11-27 13:45:10,722 - isca - INFO - -----^ 2021-11-27 13:45:10,722 - isca - INFO - /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/code/src/atmos_spectral/init/ic_from_external_file.F90(127): error #6285: There is no matching specific subroutine for this generic subroutine call. [READ_DATA] 2021-11-27 13:45:10,722 - isca - INFO - call read_data(file_name, ps_name, psg, domain=grid_domain) 2021-11-27 13:45:10,722 - isca - INFO - -----^ 2021-11-27 13:45:10,722 - isca - INFO - /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/code/src/atmos_spectral/init/ic_from_external_file.F90(137): error #6285: There is no matching specific subroutine for this generic subroutine call. [READ_DATA] 2021-11-27 13:45:10,722 - isca - INFO - call read_data(file_name, tr_name, grid_tracers(:,:,:,ntr), domain=grid_domain) 2021-11-27 13:45:10,722 - isca - INFO - -------^ 2021-11-27 13:45:10,725 - isca - INFO - compilation aborted for /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/code/src/atmos_spectral/init/ic_from_external_file.F90 (code 1) 2021-11-27 13:45:10,727 - isca - INFO - make: [ic_from_external_file.o] Error 1 2021-11-27 13:45:10,728 - isca - INFO - ERROR: mkmf failed for held_suarez.x Exception in thread background thread for pid 7309: Traceback (most recent call last): File "/home/kong97/.conda/envs/isca_env/lib/python3.9/threading.py", line 973, in _bootstrap_inner self.run() File "/home/kong97/.conda/envs/isca_env/lib/python3.9/threading.py", line 910, in run self._target(self._args, self._kwargs) File "/home/kong97/.conda/envs/isca_env/lib/python3.9/site-packages/sh.py", line 1662, in wrap fn(*args, **kwargs) File "/home/kong97/.conda/envs/isca_env/lib/python3.9/site-packages/sh.py", line 2606, in background_thread handle_exit_code(exit_code) File "/home/kong97/.conda/envs/isca_env/lib/python3.9/site-packages/sh.py", line 2304, in fn return self.command.handle_command_exit_code(exit_code) File "/home/kong97/.conda/envs/isca_env/lib/python3.9/site-packages/sh.py", line 877, in handle_command_exit_code raise exc sh.ErrorReturnCode_1:
RAN: /usr/local/bin/bash /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/build/held_suarez/compile.sh
STDOUT: load modules for isca The following modules were not unloaded: (Use "module --force purge" to unload all):
1) xalt/1.1.2 Compiling postprocessing tools load modules for isca The following modules were not unloaded: (Use "module --force purge" to unload all):
1) xalt/1.1.2 /home/kong97/.conda/envs/isca_env/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lmpifort ERROR: could not compile combine tool cb.compile() # compile the source code to working directory $GFDL_WORK/codebase File "/home/kong97/Isca/src/extra/python/isca/helpers.py", line 38, in _useworkdir return fn(*args, *kwargs) File "/home/kong97/Isca/src/extra/python/isca/helpers.py", line 22, in _destructive return fn(args, **kwargs) File "/home/kong97/Isca/src/extra/python/isca/codebase.py", line 279, in compile for line in sh.bash(P(self.builddir, 'compile.sh'), _iter=True, _err_to_out=True): File "/home/kong97/.conda/envs/isca_env/lib/python3.9/site-packages/sh.py", line 925, in next self.wait() File "/home/kong97/.conda/envs/isca_env/lib/python3.9/site-packages/sh.py", line 849, in wait self.handle_command_exit_code(exit_code) File "/home/kong97/.conda/envs/isca_env/lib/python3.9/site-packages/sh.py", line 877, in handle_command_exit_code raise exc sh.ErrorReturnCode_1:
RAN: /usr/local/bin/bash /scratch/bell/kong97/gfdl_work/codebase/_home_kong97_Isca/build/held_suarez/compile.sh
STDOUT: load modules for isca The following modules were not unloaded: (Use "module --force purge" to unload all):
1) xalt/1.1.2 Compiling postprocessing tools load modules for isca The following modules were not unloaded: (Use "module --force purge" to unload all):
1) xalt/1.1.2 /home/kong97/.conda/envs/isca_env/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lmpifort ERROR: could not compile combine tool
my env file:
Isca version
I just downloaded Isca yesterday through
git clone https://github.com/ExeClim/Isca; the latest commit should becommit 58422936f95bbe310e5cb68849a0f13d9e9c7b06System Information:
I'm using a cluster at Purdue university. We have both intel and gcc compiler. I tried to use intel compiler. However the previously installed conda and python may be compiled by gcc. Is that a problem? When I follow the install guide of Isca. I load intel compiler first, and then conda install the environment.
I have no clue where the compiling error come from. Any help is appreciated!
Thanks a lot!