Hi Yan, It looks like there is no longer an fftw/3.3.2-double module on cx2. Try loading the fftw/3.3.3-double module, recompiling and relinking Nektar++ and trying again. You can test if it is finding the library by running on the login node: ldd dist/bin/IncNavierStokesSolver | grep fftw from your build directory and see if you see a line like: libfftw3.so.3 => /apps/fftw/3.3.3/lib/libfftw3.so.3 Cheers, Chris On 29/11/14 23:46, Bao, Yan wrote:
Hi Chris,
Thanks for your email. Now, the code has been compiled successfully, However, when I qsub my job on cx2, I get the following message:
MPI: r3i3n0: 0x27c6000054417657: /home/ybao/CX2/nektar++/builds/dist/bin/IncNavierStokesSolver: error while loading shared libraries: libfftw3.so.3: cannot openMPI: r3i3n0: 0x27c6000054417657: shared object file: No such file or directory MPI: could not run executable (case #4)
In fact, I’ve loadedfftw/3.3.2-double, when running my case. Could you please help me to fix this problem? many thanks!
Regards, Yan On 29 Nov 2014, at 21:49, Chris Cantwell <c.cantwell@imperial.ac.uk <mailto:c.cantwell@imperial.ac.uk>> wrote:
Hi Yan,
It sounds like you might have exceeded your disk quota when previously compiling the code, leaving a truncated file.
If you are well within your quota, deleting the ExtractMeanModeFromHomo1DFld.cpp.o file should force it to recompile it and resolve the issue.
Cheers, Chris
On 29/11/14 21:03, Bao, Yan wrote:
Dear all,
When I’m trying to compile branch “MovingBodies” of nektar++ on cx2, I got some errors as follows:
CMakeFiles/ExtractMeanModeFromHomo1DFld.dir/ExtractMeanModeFromHomo1DFld.cpp.o: file not recognized: File truncated make[2]: *** [utilities/PostProcessing/ExtractMeanModeFromHomo1DFld-3.4.0] Error 1 make[1]: *** [utilities/PostProcessing/CMakeFiles/ExtractMeanModeFromHomo1DFld.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs….
However, the compiling process of the “master” branch is very smoothly on cx2, and I did not get any such errors when compiling my branch on victoria/euston nodes.
How can I fix it? many thanks.
Cheers, Yan
On 27 Nov 2014, at 13:57, Kamil Ozden <kamil.ozden.me@gmail.com <mailto:kamil.ozden.me@gmail.com> <mailto:kamil.ozden.me@gmail.com>> wrote:
Dear Dr. Moxey,
I got in contact with the system administrator. He told that it is impossible to recompile blas and lapack on the system with -fPIC option.
Alternatively, he copied the Blas and Lapack libraries from the directory in the system to another folder in my home directory and recompiled them there with -fPIC option.
However, when I tried to reinstall Nektar by showing the path of new Blas and Lapack libraries in my home directory I got the same error. Is there any other alternative way to overcome this problem?
Regards, Kamil
On 27-11-2014 13:10, David Moxey wrote:
Hi Kamil,
The issue is related to linking. We generate shared libraries in Nektar++, but here we are trying to link the shared library with a static library. You can only do this if the static library was compiled with the -fPIC option, which generates position-independent code that shared libraries need in order to work at runtime.
If you have a shared library, you should use this. Otherwise, you should recompile BLAS/Lapack installation with the -fPIC option. This may be something that your cluster system administrators can help with.
Thanks,
Dave
On 27 Nov 2014, at 10:37, Kamil ÖZDEN <kamil.ozden.me@gmail.com <mailto:kamil.ozden.me@gmail.com> <mailto:kamil.ozden.me@gmail.com>> wrote:
Dear All,
I'm trying to install Nektar++ 4.0 to a cluster with the options
NEKTAR_USE_BLAS_LAPACK ON NEKTAR_USE_SYSTEM_BLAS_LAPACK ON
with the path of the libraries as follows:
NATIVE_BLAS /truba/sw/centos6.4/lib/blas/netlib-gcc/blas_LINUX.a NATIVE_LAPACK /truba/sw/centos6.4/lib/lapack/netlib-3.5.0-gcc/liblapack.a
However, I'm getting the following error:
Linking CXX shared library libLibUtilities.so /usr/bin/ld: /truba/sw/centos6.4/lib/lapack/netlib-3.5.0-gcc/liblapack.a(dgbtrf.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC /truba/sw/centos6.4/lib/lapack/netlib-3.5.0-gcc/liblapack.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[2]: *** [library/LibUtilities/libLibUtilities.so.4.0.0] Error 1 make[1]: *** [library/LibUtilities/CMakeFiles/LibUtilities.dir/all] Error 2 make: *** [all] Error 2
What may be the reason for this problem and how can I solve it?
Regards, Kamil
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-- David Moxey (Research Associate) d.moxey@imperial.ac.uk <mailto:d.moxey@imperial.ac.uk><mailto:d.moxey@imperial.ac.uk> | www.imperial.ac.uk/people/d.moxey <http://www.imperial.ac.uk/people/d.moxey> <http://www.imperial.ac.uk/people/d.moxey>
Room 363, Department of Aeronautics, Imperial College London, London, SW7 2AZ, UK.
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-- Chris Cantwell Imperial College London South Kensington Campus London SW7 2AZ Email:c.cantwell@imperial.ac.uk <mailto:c.cantwell@imperial.ac.uk> www.imperial.ac.uk/people/c.cantwell <http://www.imperial.ac.uk/people/c.cantwell>
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-- Chris Cantwell Imperial College London South Kensington Campus London SW7 2AZ Email: c.cantwell@imperial.ac.uk www.imperial.ac.uk/people/c.cantwell