Dear developers,
(I appologize if you are getting multiple copies of this, I sent this email
previously using my other email address that I don’t think is in the list.)
I’m getting a NetCDF symbol error when I try to compile libMesh (commit
a58bb96d07c20eb541b557b0053269e6d8c92f15) vs PETSc 3.7.2 (commit
6d2c40479446d0366a4edb124b2d1250692ca322):
make[1]: Entering directory
`/home/mesgarnejad/Packages/libmesh/build/Linux-gnu-O'
CXXLD fparser_parse-opt
/home/mesgarnejad/Packages/petsc/Linux-gnu-O/lib/libpetsc.so: undefined
reference to `nc_def_var_deflate'
collect2: error: ld returned 1 exit status
make[1]: *** [fparser_parse-opt] Error 1
make[1]: Leaving directory
`/home/mesgarnejad/Packages/libmesh/build/Linux-gnu-O'
make: *** [all-recursive] Error 1
It’s confusing since the libpetsc.so knows where to find the correct
libnetcdf.so:
linux-vdso.so.1 => (0x00007ffce6388000)
libsuperlu_dist.so.5 =>
/home/mesgarnejad/Packages/petsc/Linux-gnu-O/lib/libsuperlu_dist.so.5
(0x00007f24966f4000)
libparmetis.so =>
/home/mesgarnejad/Packages/petsc/Linux-gnu-O/lib/libparmetis.so
(0x00007f24964b6000)
libmetis.so =>
/home/mesgarnejad/Packages/petsc/Linux-gnu-O/lib/libmetis.so
(0x00007f2496240000)
libsuperlu.so.5 =>
/home/mesgarnejad/Packages/petsc/Linux-gnu-O/lib64/libsuperlu.so.5
(0x00007f2495fc0000)
libmpi_cxx.so.1 => /shared/opt/openmpi/gcc-5.4.0/lib/libmpi_cxx.so.1
(0x00007f2495da6000)
libstdc++.so.6 => /shared/opt/gcc/lib64/libstdc++.so.6
(0x00007f2495a18000)
libhwloc.so.5 => /usr/lib64/libhwloc.so.5 (0x00007f24957d9000)
libnetcdf.so.7 =>
/home/mesgarnejad/Packages/petsc/Linux-gnu-O/lib/libnetcdf.so.7
(0x00007f24954cf000)
libhdf5hl_fortran.so.8 =>
/home/mesgarnejad/Packages/petsc/Linux-gnu-O/lib/libhdf5hl_fortran.so.8
(0x00007f24952bd000)
libhdf5_fortran.so.8 =>
/home/mesgarnejad/Packages/petsc/Linux-gnu-O/lib/libhdf5_fortran.so.8
(0x00007f2495080000)
libhdf5_hl.so.8 =>
/home/mesgarnejad/Packages/petsc/Linux-gnu-O/lib/libhdf5_hl.so.8
(0x00007f2494e51000)
libhdf5.so.8 =>
/home/mesgarnejad/Packages/petsc/Linux-gnu-O/lib/libhdf5.so.8
(0x00007f2494965000)
libX11.so.6 => /usr/lib64/libX11.so.6 (0x00007f2494627000)
libyaml-0.so.2 =>
/home/mesgarnejad/Packages/petsc/Linux-gnu-O/lib/libyaml-0.so.2
(0x00007f2494409000)
libmpi_usempif08.so.11 =>
/shared/opt/openmpi/gcc-5.4.0/lib/libmpi_usempif08.so.11 (0x00007f24941da000)
libmpi_usempi_ignore_tkr.so.6 =>
/shared/opt/openmpi/gcc-5.4.0/lib/libmpi_usempi_ignore_tkr.so.6
(0x00007f2493fd3000)
libmpi_mpifh.so.12 =>
/shared/opt/openmpi/gcc-5.4.0/lib/libmpi_mpifh.so.12 (0x00007f2493d7c000)
libgfortran.so.3 => /shared/opt/gcc/lib64/libgfortran.so.3
(0x00007f2493a5c000)
libm.so.6 => /lib64/libm.so.6 (0x00007f24937d7000)
libquadmath.so.0 => /shared/opt/gcc/lib64/libquadmath.so.0
(0x00007f2493599000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f2493395000)
libmpi.so.12 => /shared/opt/openmpi/gcc-5.4.0/lib/libmpi.so.12
(0x00007f2492e53000)
libgcc_s.so.1 => /shared/opt/gcc/lib64/libgcc_s.so.1
(0x00007f2492c3d000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f2492a20000)
libc.so.6 => /lib64/libc.so.6 (0x00007f249268b000)
librdmacm.so.1 => /usr/lib64/librdmacm.so.1 (0x00007f2492476000)
libosmcomp.so.3 => /usr/lib64/libosmcomp.so.3 (0x00007f2492268000)
libibverbs.so.1 => /usr/lib64/libibverbs.so.1 (0x00007f249205a000)
libfabric.so.1 => /usr/lib64/libfabric.so.1 (0x00007f2491dbe000)
libpsm_infinipath.so.1 => /usr/lib64/libpsm_infinipath.so.1
(0x00007f2491b6a000)
libopen-rte.so.12 =>
/shared/opt/openmpi/gcc-5.4.0/lib/libopen-rte.so.12 (0x00007f2491881000)
libtorque.so.2 => /usr/local/lib/libtorque.so.2 (0x00007f2490f9f000)
libxml2.so.2 => /usr/lib64/libxml2.so.2 (0x00007f2490c4b000)
libz.so.1 => /lib64/libz.so.1 (0x00007f2490a35000)
libcrypto.so.10 => /usr/lib64/libcrypto.so.10 (0x00007f2490655000)
libssl.so.10 => /usr/lib64/libssl.so.10 (0x00007f24903e8000)
libopen-pal.so.13 =>
/shared/opt/openmpi/gcc-5.4.0/lib/libopen-pal.so.13 (0x00007f2490100000)
libnuma.so.1 => /usr/lib64/libnuma.so.1 (0x00007f248fef7000)
librt.so.1 => /lib64/librt.so.1 (0x00007f248fcee000)
libutil.so.1 => /lib64/libutil.so.1 (0x00007f248faeb000)
/lib64/ld-linux-x86-64.so.2 (0x0000003ced000000)
libpci.so.3 => /lib64/libpci.so.3 (0x00007f248f8de000)
libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x00007f248f6c0000)
libibumad.so.3 => /usr/lib64/libibumad.so.3 (0x00007f248f4b7000)
libnl.so.1 => /lib64/libnl.so.1 (0x00007f248f265000)
libinfinipath.so.4 => /usr/lib64/libinfinipath.so.4 (0x00007f248f056000)
libgssapi_krb5.so.2 => /lib64/libgssapi_krb5.so.2 (0x00007f248ee12000)
libkrb5.so.3 => /lib64/libkrb5.so.3 (0x00007f248eb2b000)
libcom_err.so.2 => /lib64/libcom_err.so.2 (0x00007f248e927000)
libk5crypto.so.3 => /lib64/libk5crypto.so.3 (0x00007f248e6fb000)
libresolv.so.2 => /lib64/libresolv.so.2 (0x00007f248e4e0000)
libXau.so.6 => /usr/lib64/libXau.so.6 (0x00007f248e2dd000)
libkrb5support.so.0 => /lib64/libkrb5support.so.0 (0x00007f248e0d2000)
libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x00007f248dece000)
libselinux.so.1 => /lib64/libselinux.so.1 (0x00007f248dcaf000)
I attached my config.log from libMesh + you can get my configure.log
<https://www.dropbox.com/s/82yp61eequjr0p3/configure.log?dl=0>from PETSc.
Many thanks,
Ata
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