Hi,
I have installed CS 2.0-rc1 on Ubuntu 9.10 manually following the procedure in http://code-saturne.blogspot.com/2010/03/installation-of-codesaturne-20-rc1-on.html .
Preprocessor runs fine but when I start calculations I get this message:
/home/norbert/tmp_Saturne/TJUNCTION.CAS.04261327/cs_solver: error while loading shared libraries: libsaturne.so.0: cannot open shared object file: No such file or directory Error running the calculation. Check Kernel log (listing) and error* files for details
What can be the reason for this?
Best regards
Norbert
Problem with libsaturne.so.0
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-
Yvan Fournier
Re: Problem with libsaturne.so.0
Hello,
This is strange, as CS 2.0-rc1 runs fine on several Ubuntu 9.10 installs. It is possible that the install is incomplete, though I do not see why this would happen.
Could you post the compile.log file that should have appeared in your case's RESU subdirectory, to see what the final link command looked like (especially relative to -rpath options). It would also be interesting to run "ldd" on the precompiled cs_solver (the one in the install directory's bin subdirectory), and even run "./cs_solver --version" in that directory to see if the precompiled version is OK or not.
Best regards,
Yvan
This is strange, as CS 2.0-rc1 runs fine on several Ubuntu 9.10 installs. It is possible that the install is incomplete, though I do not see why this would happen.
Could you post the compile.log file that should have appeared in your case's RESU subdirectory, to see what the final link command looked like (especially relative to -rpath options). It would also be interesting to run "ldd" on the precompiled cs_solver (the one in the install directory's bin subdirectory), and even run "./cs_solver --version" in that directory to see if the precompiled version is OK or not.
Best regards,
Yvan
-
Norbert Modlinski
Re: Problem with libsaturne.so.0
Hi Yvan,
There is no compile.log in the RESU subdirectory. The only text files are summary.04261327 and listpre.(...). The second one doesn't show any error. Summary file looks like this:
PS Trying to run cs_solver gives the same: error while loading shared libraries: libsaturne.so.0....
Ldd on cs_solver gives:
linux-vdso.so.1 => (0x00007fffd77ff000)
libsaturne.so.0 => not found
libfvm.so.0 => /usr/local/lib/libfvm.so.0 (0x00007f776aa84000)
libhdf5-1.6.6.so.0 => /usr/lib/libhdf5-1.6.6.so.0 (0x00007f776a758000)
libfvm_coupl.so.0 => /usr/local/lib/libfvm_coupl.so.0 (0x00007f776a554000)
libmei.so.0 => not found
libbft.so.1 => /usr/local/lib/libbft.so.1 (0x00007f776a348000)
libz.so.1 => /lib/libz.so.1 (0x00007f776a131000)
libmpi.so.0 => /usr/lib/libmpi.so.0 (0x00007f7769e88000)
libibverbs.so.1 => /usr/lib/libibverbs.so.1 (0x00007f7769c7b000)
libpthread.so.0 => /lib/libpthread.so.0 (0x00007f7769a5f000)
libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x00007f7769817000)
libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x00007f77695a4000)
libnsl.so.1 => /lib/libnsl.so.1 (0x00007f776938a000)
libutil.so.1 => /lib/libutil.so.1 (0x00007f7769187000)
libxml2.so.2 => /usr/lib/libxml2.so.2 (0x00007f7768e37000)
libcblas.so.3gf => /usr/lib/libcblas.so.3gf (0x00007f7768c19000)
libatlas.so.3gf => /usr/lib/libatlas.so.3gf (0x00007f7768293000)
libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00007f7767fa7000)
libm.so.6 => /lib/libm.so.6 (0x00007f7767d23000)
libdl.so.2 => /lib/libdl.so.2 (0x00007f7767b1f000)
libc.so.6 => /lib/libc.so.6 (0x00007f77677b0000)
/lib64/ld-linux-x86-64.so.2 (0x00007f776ad1e000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f7767599000)
I have added "export PATH=/opt/Code_Saturne/ncs-2.0.0-rc1/bin:$PATH" line in the profile file.
Best regards,
Norbert
There is no compile.log in the RESU subdirectory. The only text files are summary.04261327 and listpre.(...). The second one doesn't show any error. Summary file looks like this:
Code: Select all
========================================================
Start time : Mon Apr 26 13:27:21 CEST 2010
----------------------------------------------------
Kernel : /usr/local
Preprocessor : /usr/local/bin
------------------------------------------------
HOMARD :
------------------------------------------------
CS_MPI_PATH : /usr/lib/openmpi/bin
PATH : /opt/Code_Saturne/ncs-2.0.0-rc1/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
------------------------------------------------
User : norbert ========================================================
Machine : Linux norbert-desktop 2.6.31-20-generic #58-Ubuntu SMP Fri Mar 12 04:38:19 UTC 2010 x86_64 GNU/Linux
N Procs : 1
Processors : default ========================================================
----------------------------------------------------
Case : CAS
DATA : /home/norbert/TJUNCTION/CAS/DATA
SRC : /home/norbert/TJUNCTION/CAS/SRC
RESU : /home/norbert/TJUNCTION/CAS/RESU
----------------------------------------------------
Exec. dir. : /home/norbert/tmp_Saturne/TJUNCTION.CAS.04261327
----------------------------------------------------
Executable : cs_solver
----------------------------------------------------
Preprocessing : yes
Partitioning : no
Calculation : failed
----------------------------------------------------
Finish time : Mon Apr 26 13:27:21 CEST 2010
========================================================
Ldd on cs_solver gives:
linux-vdso.so.1 => (0x00007fffd77ff000)
libsaturne.so.0 => not found
libfvm.so.0 => /usr/local/lib/libfvm.so.0 (0x00007f776aa84000)
libhdf5-1.6.6.so.0 => /usr/lib/libhdf5-1.6.6.so.0 (0x00007f776a758000)
libfvm_coupl.so.0 => /usr/local/lib/libfvm_coupl.so.0 (0x00007f776a554000)
libmei.so.0 => not found
libbft.so.1 => /usr/local/lib/libbft.so.1 (0x00007f776a348000)
libz.so.1 => /lib/libz.so.1 (0x00007f776a131000)
libmpi.so.0 => /usr/lib/libmpi.so.0 (0x00007f7769e88000)
libibverbs.so.1 => /usr/lib/libibverbs.so.1 (0x00007f7769c7b000)
libpthread.so.0 => /lib/libpthread.so.0 (0x00007f7769a5f000)
libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x00007f7769817000)
libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x00007f77695a4000)
libnsl.so.1 => /lib/libnsl.so.1 (0x00007f776938a000)
libutil.so.1 => /lib/libutil.so.1 (0x00007f7769187000)
libxml2.so.2 => /usr/lib/libxml2.so.2 (0x00007f7768e37000)
libcblas.so.3gf => /usr/lib/libcblas.so.3gf (0x00007f7768c19000)
libatlas.so.3gf => /usr/lib/libatlas.so.3gf (0x00007f7768293000)
libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00007f7767fa7000)
libm.so.6 => /lib/libm.so.6 (0x00007f7767d23000)
libdl.so.2 => /lib/libdl.so.2 (0x00007f7767b1f000)
libc.so.6 => /lib/libc.so.6 (0x00007f77677b0000)
/lib64/ld-linux-x86-64.so.2 (0x00007f776ad1e000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f7767599000)
I have added "export PATH=/opt/Code_Saturne/ncs-2.0.0-rc1/bin:$PATH" line in the profile file.
Best regards,
Norbert
-
Yvan Fournier
Re: Problem with libsaturne.so.0
Hello,
It would seem that libsaturne.so.0 is not present in /usr/local/lib (you can always check), while "make install" should have put it there (unless something else failed). Can you try returning to the Code_Saturne kernel (ncs) build directory, and re-run "make install", then check for libsaturne.so* in /usr/local/lib ? If it is still not there, run "make install > make.log 2>&1" and post the make.log here so that I can take a look at it.
You seem to have the same problem with libmei, so you should re-run "make && make install" in the libmei build tree first. A missing installation of MEI could explain your problem, though the ./configure stage of Code_Saturne should have failed (unless you ran "make uninstall" or did something similar between configure and make).
Best regards,
Yvan
It would seem that libsaturne.so.0 is not present in /usr/local/lib (you can always check), while "make install" should have put it there (unless something else failed). Can you try returning to the Code_Saturne kernel (ncs) build directory, and re-run "make install", then check for libsaturne.so* in /usr/local/lib ? If it is still not there, run "make install > make.log 2>&1" and post the make.log here so that I can take a look at it.
You seem to have the same problem with libmei, so you should re-run "make && make install" in the libmei build tree first. A missing installation of MEI could explain your problem, though the ./configure stage of Code_Saturne should have failed (unless you ran "make uninstall" or did something similar between configure and make).
Best regards,
Yvan
-
Norbert Modlinski
Re: Problem with libsaturne.so.0
Hi,
The think is libsaturne.so libraries are present in /usr/local/lib. They do not seem to be corrupted.
Best regards
Norbert
The think is libsaturne.so libraries are present in /usr/local/lib. They do not seem to be corrupted.
Best regards
Norbert
-
Yvan Fournier
Re: Problem with libsaturne.so.0
Hello,
Try:
export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
and then try re-running ./cs_solver
(/usr/local/lib should already be in the default library loader search path, but you may always check).
Also, in /usr/local/lib, you may compare: "file libsaturne.so.0" and "file libfvm.so.0" (if some files are symbolic links, try "file" in the file that is linked to, to get info on the file and see if anything is different).
Regards,
Yvan
Try:
export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
and then try re-running ./cs_solver
(/usr/local/lib should already be in the default library loader search path, but you may always check).
Also, in /usr/local/lib, you may compare: "file libsaturne.so.0" and "file libfvm.so.0" (if some files are symbolic links, try "file" in the file that is linked to, to get info on the file and see if anything is different).
Regards,
Yvan
-
Norbert Modlinski
Re: Problem with libsaturne.so.0
Hi,
after adding "export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH" ldd on cs_solver in /usr/local/bin shows libsaturne.so.0:
linux-vdso.so.1 => (0x00007fffc35ba000) libsaturne.so.0 => /usr/local/lib/libsaturne.so.0 (0x00007fc9cd364000) libfvm.so.0 => /usr/local/lib/libfvm.so.0 (0x00007fc9cd0c1000) (...)
Unfortunately when I run the calculations the problem appears again (home/norbert/tmp_Saturne/TJUNCTION.CAS.04261327/cs_solver: error while
loading shared libraries: libsaturne.so.0: cannot open shared object
file: No such file or directory Error running the calculation). After running cs_solver from the tmp_Saturne directory I get the following listing file:
CALCULATION PREPARATION
=======================
===========================================================
Reading file: preprocessor_output
@
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@
@ @@ WARNING: stop in data input
@ =======
@ The user subroutine 'usipph' must be completed
@ in file usini1.f90
@
@ The calculation will not be run.
@ @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@
Call stack:
1: 0x7f58fcff6be0 <usipph_+0x84> (libsaturne.so.0)
2: 0x7f58fcf323e2 <iniusi_+0x112> (libsaturne.so.0)
3: 0x7f58fcf31ea7 <initi1_+0x23> (libsaturne.so.0)
4: 0x7f58fcdcad3e <cs_run+0x9e> (libsaturne.so.0)
5: 0x7f58fcdcb7c5 <main+0x1f5> (libsaturne.so.0)
6: 0x7f58f936babd <__libc_start_main+0xfd> (libc.so.6)
7: 0x4007a9 ? (?)
End of stack
Thanks for the reply.
Regards
Norbert
after adding "export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH" ldd on cs_solver in /usr/local/bin shows libsaturne.so.0:
linux-vdso.so.1 => (0x00007fffc35ba000) libsaturne.so.0 => /usr/local/lib/libsaturne.so.0 (0x00007fc9cd364000) libfvm.so.0 => /usr/local/lib/libfvm.so.0 (0x00007fc9cd0c1000) (...)
Unfortunately when I run the calculations the problem appears again (home/norbert/tmp_Saturne/TJUNCTION.CAS.04261327/cs_solver: error while
loading shared libraries: libsaturne.so.0: cannot open shared object
file: No such file or directory Error running the calculation). After running cs_solver from the tmp_Saturne directory I get the following listing file:
CALCULATION PREPARATION
=======================
===========================================================
Reading file: preprocessor_output
@
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@
@ @@ WARNING: stop in data input
@ =======
@ The user subroutine 'usipph' must be completed
@ in file usini1.f90
@
@ The calculation will not be run.
@ @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@
Call stack:
1: 0x7f58fcff6be0 <usipph_+0x84> (libsaturne.so.0)
2: 0x7f58fcf323e2 <iniusi_+0x112> (libsaturne.so.0)
3: 0x7f58fcf31ea7 <initi1_+0x23> (libsaturne.so.0)
4: 0x7f58fcdcad3e <cs_run+0x9e> (libsaturne.so.0)
5: 0x7f58fcdcb7c5 <main+0x1f5> (libsaturne.so.0)
6: 0x7f58f936babd <__libc_start_main+0xfd> (libc.so.6)
7: 0x4007a9 ? (?)
End of stack
Thanks for the reply.
Regards
Norbert
-
Yvan Fournier
Re: Problem with libsaturne.so.0
Hello,
For some reason, it seems that the default library search path does not contain /usr/local/lib, or maybe you simply need to update the loader's cache (having root run "ldconfig" might also solve the issue).
If the issue persists, exportin LD_LIBRARY_PATH before running the Code_Saturne script should help.
The error you obtain in the temporary execution directory is "normal". Look at the contents of localexec to see the command line required, but you probably simply need to add the option --param <your_xml_file> the cs_solver to run normally.
Best regards,
Yvan
For some reason, it seems that the default library search path does not contain /usr/local/lib, or maybe you simply need to update the loader's cache (having root run "ldconfig" might also solve the issue).
If the issue persists, exportin LD_LIBRARY_PATH before running the Code_Saturne script should help.
The error you obtain in the temporary execution directory is "normal". Look at the contents of localexec to see the command line required, but you probably simply need to add the option --param <your_xml_file> the cs_solver to run normally.
Best regards,
Yvan
-
Norbert Modlinski
Re: Problem with libsaturne.so.0
Hi again,
The problem has been solved by adding /usr/local/lib to /etc/ld.so.conf then runing ldconfig.
Thanks a lot Yvan for your time and help.
Best regards
Norbert
The problem has been solved by adding /usr/local/lib to /etc/ld.so.conf then runing ldconfig.
Thanks a lot Yvan for your time and help.
Best regards
Norbert
-
Alexandre Douce
Re: Problem with libsaturne.so.0
Hi Norbert, for the error about 'usipph' see: http://code-saturne.org/forum/viewtopic.php?f=9&t=802