[petsc-users] libpciaccess dependency Problem

[Aroli Marcellinus]

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
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