Make sure your batch environment has the same modules loaded so you get the same versions of all the libraries.
Aroli Marcellinus <[email protected]> writes: > When I try to compile the program with PETSC, and run it with mpirun using > qsub. And I have checked the log and it something like this: > > cep2017_heart: error while loading shared libraries: libpciaccess.so.0: > cannot open shared object file: No such file or directory > > and I check ldd, the result is like this: > ldd bin/cep2017_heart > linux-vdso.so.1 => (0x00007fff99787000) > libsundials_cvode.so.2 => > /opt/Lib/sundials-2.7.0/lib/libsundials_cvode.so.2 (0x00002ac2b2262000) > libsundials_nvecserial.so.2 => > /opt/Lib/sundials-2.7.0/lib/libsundials_nvecserial.so.2 (0x00002ac2b248d000) > libsundials_nvecparallel.so.2 => > /opt/Lib/sundials-2.7.0/lib/libsundials_nvecparallel.so.2 > (0x00002ac2b2692000) > libX11.so.6 => /usr/lib64/libX11.so.6 (0x00000039f0c00000) > libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00002ac2b28c7000) > libdl.so.2 => /lib64/libdl.so.2 (0x00000039efc00000) > libmpi_usempif08.so.20 => > /opt/Lib/openmpi-2.1.3/lib/libmpi_usempif08.so.20 (0x00002ac2b2c6a000) > libmpi_usempi_ignore_tkr.so.20 => > /opt/Lib/openmpi-2.1.3/lib/libmpi_usempi_ignore_tkr.so.20 > (0x00002ac2b2e9d000) > libmpi_mpifh.so.20 => /opt/Lib/openmpi-2.1.3/lib/libmpi_mpifh.so.20 > (0x00002ac2b30a6000) > libmpi.so.20 => /opt/Lib/openmpi-2.1.3/lib/libmpi.so.20 > (0x00002ac2b3302000) > libifport.so.5 => > /opt/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libifport.so.5 > (0x00002ac2b35f5000) > libifcore.so.5 => > /opt/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libifcore.so.5 > (0x00002ac2b372a000) > libimf.so => > /opt/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libimf.so > (0x00002ac2b396d000) > libsvml.so => > /opt/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libsvml.so > (0x00002ac2b3d39000) > libm.so.6 => /lib64/libm.so.6 (0x00000039f0000000) > libirc.so => > /opt/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libirc.so > (0x00002ac2b44ac000) > libpthread.so.0 => /lib64/libpthread.so.0 (0x00000039f0400000) > libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00000035b0800000) > libz.so.1 => /lib64/libz.so.1 (0x00000037c7600000) > libc.so.6 => /lib64/libc.so.6 (0x00000039ef800000) > libXau.so.6 => /usr/lib64/libXau.so.6 (0x00000039f0800000) > libXdmcp.so.6 => /usr/lib64/libXdmcp.so.6 (0x00000039f1000000) > /lib64/ld-linux-x86-64.so.2 (0x00000039ef000000) > libopen-rte.so.20 => /opt/Lib/openmpi-2.1.3/lib/libopen-rte.so.20 > (0x00002ac2b45fb000) > libopen-pal.so.20 => /opt/Lib/openmpi-2.1.3/lib/libopen-pal.so.20 > (0x00002ac2b4884000) > libpciaccess.so.0 => /usr/lib64/libpciaccess.so.0 (0x00002ac2b4b86000) > librt.so.1 => /lib64/librt.so.1 (0x00000039f3c00000) > libutil.so.1 => /lib64/libutil.so.1 (0x00000039fca00000) > libintlc.so.5 => > /opt/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libintlc.so.5 > (0x00002ac2b4d8d000) > libifcoremt.so.5 => > /opt/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libifcoremt.so.5 > (0x00002ac2b4eda000) > > > So as you can see that the libpciaccess already coupled to the compiled > program, but it's still error. So I know that libpciaccess maybe from the > MPI libs (I'm using OpenMPI), but this kind of error is really bugging me. > > Even after I tried to use --disable-hwloc-pci when installing OpenMPI, it > still got this kind of error,. > > What I want to know is: > - Is it possible to remove the dependenciness of libpciaccess? > - Or how to configure it so that PETSc or MPI doesn't use libpciaccess? > > In my case, I cannot use static because some of those dependencies doesn't > have static libraries. > > I'm using: > PETSc-3.9.0 > OpenMPI-2.1.3 > > > > > Aroli Marcellinus > > *Kumoh Institute of Technology**Computational Medicine Laboratory* > 61 Daehak-ro (Sinpyeong-dong), Gumi, Gyeongbuk > +82 10 9724 3957 > KTalk ID: vondarkness
