Re: [OMPI users] MPI libraries

OK. I will try that. Thanks for the suggestion. Regards, Mahmood On Mon, Sep 12, 2016 at 11:35 PM, Dave Love wrote: > Gilles Gouaillardet writes: > > > Mahmood, > > > > mpi_siesta is a siesta library, not an Open MPI library. > > > >

Re: [OMPI users] MPI libraries

Gilles Gouaillardet writes: > Mahmood, > > mpi_siesta is a siesta library, not an Open MPI library. > > fwiw, you might want to try again from scratch with > MPI_INTERFACE=libmpi_f90.a > DEFS_MPI=-DMPI > in your arch.make > > i do not think libmpi_f90.a is related

Re: [OMPI users] MPI libraries

It might be easier to not list the MPI library that Open MPI is using -- we have changed the name of this library over time (as you have noticed). The "mpifort" wrapper compiler will always pick up the right library name for you. > On Sep 12, 2016, at 1:44 PM, Mahmood Naderan

Re: [OMPI users] MPI libraries

>i do not think libmpi_f90.a is related to an OpenMPI library. Thing is that, libmpi_f90.a is part of 1.6.5 and siesta use that. However, 1.8.8 has no such file. Instead it has some other names and you said before that mpifort (the wrapper) will automatically use the necessary libraries. Please

Re: [OMPI users] MPI libraries

Mahmood, mpi_siesta is a siesta library, not an Open MPI library. fwiw, you might want to try again from scratch with MPI_INTERFACE=libmpi_f90.a DEFS_MPI=-DMPI in your arch.make i do not think libmpi_f90.a is related to an OpenMPI library. if you need some more support, please refer to the

[OMPI users] MPI libraries

Hi, Trying to build a source code with newer versions of OpenMPI, I still have some problems that weren't exist in previous versions. In 1.6.5, I wrote something in a arch.make file which is used by Makefile FC=/export/apps/siesta/openmpi-1.6.5/bin/mpif90 MPI_INTERFACE=libmpi_f90.a MPI_INCLUDE=.

Re: [OMPI users] Problem with specifying wrapper compiler mpifort

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.

Re: [hwloc-users] memory binding on Knights Landing

Brice Goglin writes: > So what's really slow is reading sysfs and/or inserting all hwloc > objects in the tree. I need to do some profiling. And I am moving the > item "parallelize the discovery" higher in the TODO list :) It didn't seem to scale between systems with the

Re: [OMPI users] Problem with specifying wrapper compiler mpifort

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

Re: [OMPI users] Problem with specifying wrapper compiler mpifort

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

Re: [OMPI users] Problem with specifying wrapper compiler mpifort

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

Re: [OMPI users] Problem with specifying wrapper compiler mpifort

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

Re: [OMPI users] Problem with specifying wrapper compiler mpifort

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:

Re: [OMPI users] Problem with specifying wrapper compiler mpifort

>​ --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

Re: [OMPI users] Problem with specifying wrapper compiler mpifort

>​ --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 ___ users mailing list users@lists.open-mpi.org

Re: [OMPI users] Problem with specifying wrapper compiler mpifort

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*

Re: [OMPI users] Problem with specifying wrapper compiler mpifort

​>(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

Re: [OMPI users] Problem with specifying wrapper compiler mpifort

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

[OMPI users] Problem with specifying wrapper compiler mpifort

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