Re: "nfaced" with periodic boundaries
Posted: Mon Nov 11, 2013 6:12 pm
Hello Yvan,
Thank you so much for your reply. I've installed the code with Metis-5.0.2. I followed your instructions and the new logged "configure" command is now the following:
r01ken0/Code_Saturne/v2.0.5/installer/ecs-2.0.2/configure --prefix=/users/r01ken0/Code_Saturne/v2.0.5/cs-2.0 --with-bft=/users/r01ken0/Code_Saturne/v2.0.5/cs-2.0 --with-hdf5=/users/r01ken0/Code_Saturne/opt --with-cgns=/users/r01ken0/Code_Saturne/opt --with-med=/users/r01ken0/Code_Saturne/opt --with-metis=/users/r01ken0/Code_Saturne/opt CC=gcc --enable-long-int
However, this has still not solved the problem. When I run "code_saturne mesh_check -m meshname.cgns" I obtain the following error in the terminal and in an error file:
***************************************************************
Local case configuration:
Date: Mon 11 Nov 2013 15:25:45 GMT
System: Linux 2.6.32-279.14.1.el6.x86_64
Machine: vhmem01
Processor: Intel(R) Xeon(R) CPU E7- 4820 @ 2.00GHz
Memory: 1033945 MB
User: r01ken0
Directory: /users/r01ken0/simulations/60degree_bundle_OLD/MESH
MPI ranks: 1
===============================================================
CALCULATION PREPARATION
=======================
===========================================================
Reading file: preprocessor_output
/users/r01ken0/Code_Saturne/v2.0.5/installer/bft-1.1.5/src/bft_file.c:794: Fatal error.
Error opening file "preprocessor_output":
No such file or directory
Call stack:
1: 0x2b3bfe7cd177 <bft_file_open_stream+0xa7> (libbft.so.1)
2: 0x2b3bfe7cd3a6 <bft_file_open+0xa6> (libbft.so.1)
3: 0x2b3bfd69a020 <fvm_file_open+0x140> (libfvm.so.0)
4: 0x2b3bfc35133b <+0xb033b> (libsaturne.so.0)
5: 0x2b3bfc352323 <cs_io_initialize+0x93> (libsaturne.so.0)
6: 0x2b3bfc3eeec9 <ledevi_+0x79> (libsaturne.so.0)
7: 0x2b3bfc43b557 <iniini_+0xce3> (libsaturne.so.0)
8: 0x2b3bfc43e2ae <initi1_+0x16> (libsaturne.so.0)
9: 0x2b3bfc2c5688 <cs_run+0xa8> (libsaturne.so.0)
10: 0x2b3bfc2c6105 <main+0x1f5> (libsaturne.so.0)
11: 0x34d101ecdd <__libc_start_main+0xfd> (libc.so.6)
12: 0x400739 <> (cs_solver)
End of stack
Traceback (most recent call last):
File "/users/r01ken0/Code_Saturne/v2.0.5/cs-2.0/bin/code_saturne", line 127, in <module>
main(sys.argv[1:])
File "/users/r01ken0/Code_Saturne/v2.0.5/cs-2.0/bin/code_saturne", line 122, in main
commands[command](argv[1:])
File "/users/r01ken0/Code_Saturne/v2.0.5/cs-2.0/bin/code_saturne", line 71, in check_mesh
cs_check_mesh.main(argv)
File "/users/r01ken0/Code_Saturne/v2.0.5/cs-2.0/lib/python2.6/site-packages/ncs/cs_check_mesh.py", line 112, in main
retcode = run_check(argv)
File "/users/r01ken0/Code_Saturne/v2.0.5/cs-2.0/lib/python2.6/site-packages/ncs/cs_check_mesh.py", line 91, in run_check
dir_files = os.listdir('chr.ensight')
OSError: [Errno 2] No such file or directory: 'chr.ensight'
In the .log file (attached) it mentions a memory allocation error. I've made sure I have memory quota on the cluster and I don't really know what else to do. Any other suggestions?
Thank you,
Kristin
Thank you so much for your reply. I've installed the code with Metis-5.0.2. I followed your instructions and the new logged "configure" command is now the following:
r01ken0/Code_Saturne/v2.0.5/installer/ecs-2.0.2/configure --prefix=/users/r01ken0/Code_Saturne/v2.0.5/cs-2.0 --with-bft=/users/r01ken0/Code_Saturne/v2.0.5/cs-2.0 --with-hdf5=/users/r01ken0/Code_Saturne/opt --with-cgns=/users/r01ken0/Code_Saturne/opt --with-med=/users/r01ken0/Code_Saturne/opt --with-metis=/users/r01ken0/Code_Saturne/opt CC=gcc --enable-long-int
However, this has still not solved the problem. When I run "code_saturne mesh_check -m meshname.cgns" I obtain the following error in the terminal and in an error file:
***************************************************************
Local case configuration:
Date: Mon 11 Nov 2013 15:25:45 GMT
System: Linux 2.6.32-279.14.1.el6.x86_64
Machine: vhmem01
Processor: Intel(R) Xeon(R) CPU E7- 4820 @ 2.00GHz
Memory: 1033945 MB
User: r01ken0
Directory: /users/r01ken0/simulations/60degree_bundle_OLD/MESH
MPI ranks: 1
===============================================================
CALCULATION PREPARATION
=======================
===========================================================
Reading file: preprocessor_output
/users/r01ken0/Code_Saturne/v2.0.5/installer/bft-1.1.5/src/bft_file.c:794: Fatal error.
Error opening file "preprocessor_output":
No such file or directory
Call stack:
1: 0x2b3bfe7cd177 <bft_file_open_stream+0xa7> (libbft.so.1)
2: 0x2b3bfe7cd3a6 <bft_file_open+0xa6> (libbft.so.1)
3: 0x2b3bfd69a020 <fvm_file_open+0x140> (libfvm.so.0)
4: 0x2b3bfc35133b <+0xb033b> (libsaturne.so.0)
5: 0x2b3bfc352323 <cs_io_initialize+0x93> (libsaturne.so.0)
6: 0x2b3bfc3eeec9 <ledevi_+0x79> (libsaturne.so.0)
7: 0x2b3bfc43b557 <iniini_+0xce3> (libsaturne.so.0)
8: 0x2b3bfc43e2ae <initi1_+0x16> (libsaturne.so.0)
9: 0x2b3bfc2c5688 <cs_run+0xa8> (libsaturne.so.0)
10: 0x2b3bfc2c6105 <main+0x1f5> (libsaturne.so.0)
11: 0x34d101ecdd <__libc_start_main+0xfd> (libc.so.6)
12: 0x400739 <> (cs_solver)
End of stack
Traceback (most recent call last):
File "/users/r01ken0/Code_Saturne/v2.0.5/cs-2.0/bin/code_saturne", line 127, in <module>
main(sys.argv[1:])
File "/users/r01ken0/Code_Saturne/v2.0.5/cs-2.0/bin/code_saturne", line 122, in main
commands[command](argv[1:])
File "/users/r01ken0/Code_Saturne/v2.0.5/cs-2.0/bin/code_saturne", line 71, in check_mesh
cs_check_mesh.main(argv)
File "/users/r01ken0/Code_Saturne/v2.0.5/cs-2.0/lib/python2.6/site-packages/ncs/cs_check_mesh.py", line 112, in main
retcode = run_check(argv)
File "/users/r01ken0/Code_Saturne/v2.0.5/cs-2.0/lib/python2.6/site-packages/ncs/cs_check_mesh.py", line 91, in run_check
dir_files = os.listdir('chr.ensight')
OSError: [Errno 2] No such file or directory: 'chr.ensight'
In the .log file (attached) it mentions a memory allocation error. I've made sure I have memory quota on the cluster and I don't really know what else to do. Any other suggestions?
Thank you,
Kristin