OK. Running "module unload rocks-openmpi" and putting that in ~/.bashrc
will remove /opt/openmpi/lib from LD_LIBRARY_PATH.
Thanks Gilles for your help.
Regards,
Mahmood
On Mon, Sep 12, 2016 at 1:25 PM, Mahmood Naderan
wrote:
> It seems that it is part of rocks-openmpi. I will find out how to
It seems that it is part of rocks-openmpi. I will find out how to remove it
and will come back.
Regards,
Mahmood
On Mon, Sep 12, 2016 at 1:06 PM, Gilles Gouaillardet
wrote:
> Mahmood,
>
> you need to manually remove /opt/openmpi/lib from your LD_LIBRARY_PATH
> (or have your sysadmin do it if
Mahmood,
you need to manually remove /opt/openmpi/lib from your LD_LIBRARY_PATH
(or have your sysadmin do it if this is somehow done automatically)
the point of configuring with --enable-mpirun-prefix-by-default is you
do *not* need
to add /export/apps/siesta/openmpi-1.8.8/lib in your LD_LIBRA
Is the following output OK?
...
Making install in util
make[2]: Entering directory `/export/apps/siesta/openmpi-1.8.8/test/util'
make[3]: Entering directory `/export/apps/siesta/openmpi-1.8.8/test/util'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-da
Mahmood,
I was suggesting you (re)configure (i assume you did it) the Open MPI
1.8.8 installed in /export/apps/siesta/openmpi-1.8.8 with
--enable-mpirun-prefix-by-default
Cheers,
Gilles
On 9/12/2016 4:51 PM, Mahmood Naderan wrote:
> --enable-mpirun-prefix-by-default
What is that? Does t
Basically, it means libs with be linked with
-Wl,-rpath,/export/apps/siesta/openmpi-1.8.8/lib
so if you run a.out with an empty $LD_LIBRARY_PATH, then it will look
for the MPI libraries in
/export/apps/siesta/openmpi-1.8.8/lib
Cheers,
Gilles
On 9/12/2016 4:50 PM, Mahmood Naderan wrote:
> --enable-mpirun-prefix-by-default
What is that? Does that mean "configure 1.8.8 with the default one
installed on the system"? Then that is not good I think because
# /opt/openmpi/bin/ompi_info
Package: Open MPI root@centos-6-3.localdomain Distribution
O
> --enable-mpirun-prefix-by-default
What is that? Does that mean "configure 1.8.8 with the default one
installed on the system"? Then that is not good I think because
Regards,
Mahmood
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That sounds good to me !
just to make it crystal clear ...
assuming you configure'd your Open MPI 1.8.8 with
--enable-mpirun-prefix-by-default
(and if you did not, i do encourage you to do so), then all you need is
to remove
/opt/openmpi/lib from your LD_LIBRARY_PATH
(e.g. you do *not* ha
>(i'd like to make sure you are not using IntelMPI libmpi.so.1 with Open
MPI libmpi_mpifh.so.2, that can happen if Intel MPI >appears first in your
LD_LIBRARY_PATH)
# echo $LD_LIBRARY_PATH
/opt/gridengine/lib/linux-x64:/opt/openmpi/lib
# ls /opt/openmpi/lib
libmpi.a libompitrace.a
Hi,
this is the relevant part of your config.log
configure:1594: checking whether the Fortran compiler works
configure:1600: ./a.out
./a.out: symbol lookup error:
/export/apps/siesta/openmpi-1.8.8/lib/libmpi_mpifh.so.2: undefined
symbol: mpi_fortran_weights_empty
configure:1603: $? = 127
c
Hi,
Following the suggestion by Gilles Gouaillardet (
https://mail-archive.com/users@lists.open-mpi.org/msg29688.html), I ran a
configure command for a program like this
# ../Src/configure FC=/export/apps/siesta/openmpi-1.8.8/bin/mpifort
--with-blas=libopenblas.a --with-lapack=liblapack.a
--with-
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