[OMPI users] Low cpu utilization due to high IO operations of openmpi

Dear all, We have a diskless cluster with these specs: 1) A server which has some disks. Root directories (/usr, /lib, ...) are on /dev/sda while /home is on /dev/sdb and these are two physical hard drives. 2) Some compute nodes. These don't have any disk drive instead they are connected

[OMPI users] running openmpi in debug/verbose mode

Dear all, Is there any way to run openmpi in debug or verbose mode? Is there any log for openmpi run?   Regards, Mahmood

Re: [OMPI users] running openmpi in debug/verbose mode

From: Ralph Castain <r...@open-mpi.org> To: Mahmood Naderan <nt_mahm...@yahoo.com>; Open MPI Users <us...@open-mpi.org> Sent: Thursday, October 25, 2012 8:44 PM Subject: Re: [OMPI users] running openmpi in debug/verbose mode There is a *ton* of debug output available - would

Re: [OMPI users] running openmpi in debug/verbose mode

lph Castain <r...@open-mpi.org> To: Mahmood Naderan <nt_mahm...@yahoo.com> Sent: Thursday, October 25, 2012 8:55 PM Subject: Re: [OMPI users] running openmpi in debug/verbose mode Sorry - we're all a tad busy with deadlines for the Supercomputing conference :-( You are probably runni

[OMPI users] openmpi shared memory feature

Dear all, Why openmpi uses shared memory model? this can be disabled though by setting "--mca ^sm".  It seems that by default openmpi uses such feature (shared memory backing files) which is strange.   Regards, Mahmood

Re: [OMPI users] open mpi 1.6 with intel compilers

>This looks like you're trying to execute an MPICH2-build MPI executable, not >Open MPI. No that was a general question. I mean message passing is a model of communication versus shared memory programming. So what is the point when openmpi uses shared memory model?   Regards, Mahmood

Re: [OMPI users] open mpi 1.6 with intel compilers

oops... Sorry about that.   Regards, Mahmood From: Jeff Squyres <jsquy...@cisco.com> To: Mahmood Naderan <nt_mahm...@yahoo.com>; Open MPI Users <us...@open-mpi.org> Sent: Saturday, October 27, 2012 6:34 PM Subject: Re: [OMPI users] open

Re: [OMPI users] openmpi shared memory feature

ase, their communication go though network (from computing node to server) then IO and then network again (from server to computing node). Regards, Mahmood From: Jeff Squyres <jsquy...@cisco.com> To: Mahmood Naderan <nt_mahm...@yahoo.com>; Open MPI Us

Re: [OMPI users] openmpi shared memory feature

rate because it's more efficient. Damien On 27/10/2012 11:00 AM, Jeff Squyres wrote: > On Oct 27, 2012, at 12:47 PM, Mahmood Naderan wrote: > >>> Because communicating through shared memory when sending messages between >>> processes on the same server is far faster tha

Re: [OMPI users] openmpi shared memory feature

on that.   Regards, Mahmood From: Jeff Squyres <jsquy...@cisco.com> To: Mahmood Naderan <nt_mahm...@yahoo.com>; Open MPI Users <us...@open-mpi.org> Sent: Monday, October 29, 2012 1:28 PM Subject: Re: [OMPI users] openmpi shared memory featur

Re: [OMPI users] openmpi shared memory feature

I have understood about the the advantages of shared memeory BTL. I wanted to share some of my observations and gain an understanding about the internal mechanisms of opemmpi. I am wondering why openmpi uses a temporary file for transferring data between the two processes which are on the same

[OMPI users] Need libmpi_f90.a

Hi, I need libmpi_f90.a for building an application. I have manually compiled 1.6.5 and 1.10.3 but that file is absent. Instead I see these openmpi-1.6.5/lib/libmpi_f90.la openmpi-1.10.3/lib/libmpi_mpifh.la What should I do? Regards, Mahmood

Re: [OMPI users] Need libmpi_f90.a

>./configure --disable-shared --enable-static Thank you very much Regards, Mahmood

Re: [OMPI users] Need libmpi_f90.a

5 -> libmpi_usempi.so.5.1.0 -rwxr-xr-x 1 root root 11900 Jul 11 23:51 libmpi_usempi.so.5.1.0 Regards, Mahmood On Sun, Jul 10, 2016 at 8:39 PM, Mahmood Naderan <mahmood...@gmail.com> wrote: > >./configure --disable-shared --enable-static > > Thank you very much > > Regards, > Mahmood > >

Re: [OMPI users] Need libmpi_f90.a

Sorry but I didn't understand the relation between name changes and wrapper compilers. I only used --enable-static in the configure process. > -rw-r--r-- 1 root root 1029580 Jul 11 23:51 libmpi_mpifh.a > -rw-r--r-- 1 root root 17292 Jul 11 23:51 libmpi_usempi.a >These are the two for v1.10.x.

Re: [OMPI users] job aborts "readv failed: Connection reset by peer"

>Did you ran >ulimit -c unlimited >before invoking mpirun ? Yes. On the node which says that error. Is that file created in the current working directory? Or it is somewhere in the system folders? As another question, I am trying to use OpenMPI-2.0.0 as a new one. Problem is that the

Re: [OMPI users] job aborts "readv failed: Connection reset by peer"

The application is Siesta-3.2 and the command I use is /share/apps/computer/openmpi-1.6.5/bin/mpirun -hostfile hosts.txt -np 15 /share/apps/chemistry/siesta-3.2-pl-5/tpar/transiesta < trans-cc-bt-cc-163-20.fdf There is one node in the hosts.txt file. I have built transiesta binary from the

Re: [OMPI users] job aborts "readv failed: Connection reset by peer"

Thanks for your help. Please see below mahmood@compute-0-1:~$ ldd /share/apps/chemistry/siesta-3.2-pl-5/tpar/transiesta linux-vdso.so.1 => (0x7fffba9a8000) libmpi_f90.so.1 => /opt/openmpi/lib/libmpi_f90.so.1 (0x2b472b64) libmpi_f77.so.1 =>

[OMPI users] Error in file runtime/orte_init.c

Hi, Using OpenMPI-2.0.0, is there any idea about this error A requested component was not found, or was unable to be opened. This means that this component is either not installed or is unable to be used on your system (e.g., sometimes this means that shared libraries that the component requires

Re: [OMPI users] Error in file runtime/orte_init.c

​OK thanks for the hint. In fact 'ldd' command shows that some libraries were missing. adding the paths to LD_LIBRARY_PATH solved the problem. Regards, Mahmood ___ users mailing list users@lists.open-mpi.org

Re: [OMPI users] job aborts "readv failed: Connection reset by peer"

>Are you running under a batch manager ? >On which architecture ? Currently I am not using the job manager (which is actually PBS). I am running from the terminal. The machines are AMD Opteron 64 bit >Hopefully you will get a core file that points you to the illegal instruction Where is that

[OMPI users] job aborts "readv failed: Connection reset by peer"

Hi, An MPI job is running on two nodes and everything seems to be fine. However, in the middle of the run, the program aborts with the following error [compute-0-1.local][[47664,1],14][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)

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

[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

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

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_LIBRARY_PATH > > Cheers, > > Gilles > &g

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

​>(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

Distribution Open MPI: 1.6.2 Regards, Mahmood On Mon, Sep 12, 2016 at 12:20 PM, Mahmood Naderan <mahmood...@gmail.com> wrote: > >​ --enable-mpirun-prefix-by-default​ > > What is that? Does that mean "configure 1.8.8 with the default one > installed on the

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 <mahmood...@gmail.com> wrote: > It seems that it is pa

[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] static linking MPI libraries with applications

Do you mean --disable-dl-dlopen? The last lines of configure are +++ Configuring MCA framework dl checking for no configure components in framework dl... checking for m4 configure components in framework dl... libltdl, dlopen --- MCA component dl:dlopen (m4 configuration macro, priority 80)

[OMPI users] static linking MPI libraries with applications

Hi, Here is the problem with statically linking an application with a program. by specifying the library names: FC=/export/apps/siesta/openmpi-1.8.8/bin/mpifort FFLAGS=-g -Os FPPFLAGS= -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT LDFLAGS=-static MPI1=/export/apps/siesta/openmpi-1.8.8/lib/libmpi_mpifh.a

Re: [OMPI users] static linking MPI libraries with applications

d /export/apps/siesta/openmpi-1.8.8/lib to your > $LD_LIBRARY_PATH > > note this is not required when Open MPI is configure'd with > --enable-mpirun-prefix-by-default > > > Cheers, > > Gilles > > On Wednesday, September 14, 2016, Mahmood Naderan <mahmo

Re: [OMPI users] MPI libraries

It seems that siesta build its own mpi library named libmpi_f90.a which has the same name as MPI's libraries. I solved it. Thanks for all suggestions. Regards, Mahmood ___ users mailing list users@lists.open-mpi.org

Re: [OMPI users] static linking MPI libraries with applications

So, I used ./configure --prefix=/export/apps/siesta/openmpi-1.8.8 --enable-mpirun-prefix-by-default --enable-static --disable-shared --disable-dlopen and added -static to LDFLAGS, but I get: /export/apps/siesta/openmpi-1.8.8/bin/mpifort -o transiesta -static libfdf.a libSiestaXC.a \

Re: [OMPI users] static linking MPI libraries with applications

​I installed libibverb-devel-static.x86_64 via yum root@cluster:tpar# yum list libibverb* Installed Packages libibverbs.x86_64 1.1.8-4.el6@base libibverbs-devel.x86_64 1.1.8-4.el6@base libibverbs-devel-static.x86_64 1.1.8-4.el6

Re: [OMPI users] static linking MPI libraries with applications

Good news :) >If I drop -static, the error is gone... However, ldd command shoes that binary can not access those two MPI libraries. In the previous installation, I kept both .so and .a files. Therefore, it first searched for .so files and that was the reason why ldd failed. Forget about

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

>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] OMPI users] Still "illegal instruction"

Although the CPUs are nearly the same, but the CPU flags are different. I noticed that the frontend has fma, f16c, tch, tce, tbm and bmi1 while the compute nodes don't have them. I guess that since the programs were compiled on the frontend (6380), there are some especial instructions in the

Re: [OMPI users] OMPI users] Still "illegal instruction"

Excuse me, which is most suitable for me to find the name of the illegal instruction? --verbose --debug-level --debug-daemons --debug-daemons-file Regards, Mahmood ___ users mailing list users@lists.open-mpi.org

Re: [OMPI users] OMPI users] Still "illegal instruction"

The differences are very very minor root@cluster:tpar# echo | gcc -v -E - 2>&1 | grep cc1 /usr/libexec/gcc/x86_64-redhat-linux/4.4.7/cc1 -E -quiet -v - -mtune=generic [root@compute-0-1 ~]# echo | gcc -v -E - 2>&1 | grep cc1 /usr/libexec/gcc/x86_64-redhat-linux/4.4.6/cc1 -E -quiet -v -

Re: [OMPI users] OMPI users] Still "illegal instruction"

OK Gilles, let me try that. I will troubleshoot with gcc mailing list and will come back later. Regards, Mahmood ___ users mailing list users@lists.open-mpi.org https://rfd.newmexicoconsortium.org/mailman/listinfo/users

Re: [OMPI users] not enough slots available

n Wed, Oct 5, 2016 at 7:52 PM, Mahmood Naderan <mahmood...@gmail.com> wrote: > Sorry about the incomplete message... > > Is there any idea about the following error? On that node, there are 15 > empty cores. > > $ /share/apps/siesta/openmpi-2.0.1/bin/mpirun --host comp

[OMPI users] (no subject)

Hi, Is there any idea about the following error? On that node, there are 15 empty cores. Regards, Mahmood ___ users mailing list users@lists.open-mpi.org https://rfd.newmexicoconsortium.org/mailman/listinfo/users

[OMPI users] not enough slots available

Sorry about the incomplete message... Is there any idea about the following error? On that node, there are 15 empty cores. $ /share/apps/siesta/openmpi-2.0.1/bin/mpirun --host compute-0-3 -np 2 /share/apps/siesta/siesta-4.0-mpi201/tpar/transiesta < A.fdf

Re: [OMPI users] OMPI users] Still "illegal instruction"

disas command fails. Program terminated with signal 4, Illegal instruction. #0 0x008da76e in ?? () (gdb) bt #0 0x008da76e in ?? () #1 0x008da970 in ?? () #2 0x00bfe9f8 in ?? () #3 0x in ?? () (gdb) disas No function contains program counter for

[OMPI users] Still "illegal instruction"

Hi, After upgrading OpenMPI (from 1.6.5 to 2.0.0) and my program (from 3.2 to 4.0), still the parallel run aborts with the "Illegal instruction" error in the middle on the run. I wonder why this happens and how can I debug more? How can I find that this error is related to the program itself, mpi

Re: [OMPI users] Still "illegal instruction"

>gdb --pid=core.5383 ​Are you sure about the syntax?​ ​PID must be a running process. I see --core which seems to be relevant here. Both OpenMPI and Siesta were compiled with O flags. This is not appropriate for gdb. Should I compile both of them with debug symbols? >Btw, did you compile lapack

Re: [OMPI users] OMPI users] Still "illegal instruction"

Dear Gilles, It seems that using GDB with MPI is a bit tricky. I read the FAQ about that. Please see the post at https://gcc.gnu.org/ml/gcc-help/2016-09/msg00078.html >i guess your gdb is also a bit too old to support all operations on a core file >(fwiw, i am able to do that on RHEL7) This is

Re: [OMPI users] OMPI users] Still "illegal instruction"

​>Thx for sharing, quite interesting. But does this mean, that there is no working command line flag for gcc to switch this >off (like -march=bdver1 what Gilles mentioned) or to tell me what he thinks it should compile for? ​ Well that didn't work. maybe I messed somethings since I did recompile

[OMPI users] Multiple versions of OpenMPI

Hello, Consider that OMPI-2.0.1 has been installed with --enable-mpirun-prefix-by-default. Now, is it possible to install OMPI-1.6.5 in its own folder and use it without any problem? I mean, if I run ompi-1.6.5/bin/mpirun, I want to be sure that ompi-2.0.1/lib is not in use. Please let me know,

Re: [OMPI users] Viewing the output of the program

> Cheers, > > Gilles > > > On Saturday, October 1, 2016, Mahmood Naderan <mahmood...@gmail.com> > wrote: > >> Hi, >> Here is the bizarre behavior of the system and hope that someone can >> clarify is this related to OMPI or not. >> >> When I i

[OMPI users] Problem running an MPI program through the PBS manager

Hi, When I run an MPI command through the terminal the programs runs fine on the compute node specified in hosts.txt. However, when I put that command in a PBS script, if says that the compute node is not defined in the job manager's list. However, that node is actually defined in the job

Re: [OMPI users] Problem running an MPI program through the PBS manager

list of allocated nodes is in the file $PBS_NODEFILE, but you > should not need that. > > Cheers, > > Gilles > > > On Monday, September 26, 2016, Mahmood Naderan <mahmood...@gmail.com> > wrote: > >> Hi, >> When I run an MPI command through the terminal the

[OMPI users] Viewing the output of the program

Hi, Here is the bizarre behavior of the system and hope that someone can clarify is this related to OMPI or not. When I issue the mpirun command with -np 2, I can see the output of the program online as it is running (I am std out). However, if I issue the command with -np 4, the progress is not

Re: [OMPI users] error on dlopen

>​What problems are you referring to? I mean errors that are saying failed to load X.so. Then the user has to add some paths to LD_LIBRARY_PATH. Although such problem can be fixed by adding an export to the .bashrc, but I prefer to avoid that. >We might need a bit more detail than that; I use

[OMPI users] An old code compatibility

Hi, The following mpifort command fails with a syntax error. It seems that the code is compatible with old gfortran, but I am not aware of that. Any idea about that? mpifort -ffree-form -ffree-line-length-0 -ff2c -fno-second-underscore -I/opt/fftw-3.3.5/include -O3 -c xml.f90 xml.F:641.46:

[OMPI users] Using custom version of gfortran in mpifort

Hi, The mpifort wrapper uses the default gfortran compiler on the system. How can I give it another version of gfortran which has been installed in another folder? Regards, Mahmood ___ users mailing list users@lists.open-mpi.org

Re: [OMPI users] An old code compatibility

The output is not meaningful for me. If I add --showme option, the output is http://pastebin.com/FX1ks8iW and if I drop --showme, the output is http://pastebin.com/R1QFYVBe Please search for xml.F. Do you have any idea? Regards, Mahmood ___ users

[OMPI users] error on dlopen

Hi I am building scalapack with mpicc and mpifort, however this is the error I get: mpifort -O3 -o xCbtest blacstest.o btprim.o tools.o Cbt.o ../../libscalapack.a /opt/openmpi-2.0.1/lib/libopen-pal.a(dl_dlopen_module.o): In function `dlopen_close': dl_dlopen_module.c:(.text+0x29d): undefined

Re: [OMPI users] error on dlopen

I will try that. Meanwhile, I want to know what is the performance effect of disabling/enabling dlopen? Regards, Mahmood On Fri, Nov 4, 2016 at 11:02 AM, Gilles Gouaillardet wrote: > Yes, that is a problem :-( > > > you might want to reconfigure with > > --enable-static

Re: [OMPI users] error on dlopen

Hi Gilles, I noticed that /opt/openmpi-2.0.1/share/openmpi/mpifort-wrapper-data.txt is created after "make install". So, I edited it and appended -ldl to libs_static. Then I ran "make clean && make all" for scalapack. However, still get the same error!! So, let me try disabling dlopen.

Re: [OMPI users] error on dlopen

, Sean Ahern <s...@ensight.com> wrote: > Sounds to me like you're missing a -ldl linker flag. > > -Sean > > -- > Sean Ahern > Computational Engineering International > 919-363-0883 > > On Thu, Nov 3, 2016 at 3:57 PM, Mahmood Naderan <mahmood...@gmail.com> &

Re: [OMPI users] error on dlopen

>did you build Open MPI as a static only library ? Yes, I used --enable-static --disable-shared Please see the output # mpifort -O3 -o xCbtest --showme blacstest.o btprim.o tools.o Cbt.o ../../libscalapack.a -ldl gfortran -O3 -o xCbtest blacstest.o btprim.o tools.o Cbt.o ../../libscalapack.a

Re: [OMPI users] error on dlopen

> You might have to remove -ldl from the scalapack makefile I removed that before... I will try one more time Actually, using --disable-dlopen fixed the error. >mpirun --showme $ mpirun --showme mpirun: Error: unknown option "--showme" Type 'mpirun --help' for usage. Regards, Mahmood On

Re: [OMPI users] error on dlopen

>​If there's a reason you did --enable-static --disable-shared​ Basically, I want to prevent dynamic library problems (ldd) on a distributed environment. ​$ mpifort --showme gfortran -I/opt/openmpi-2.0.1/include -pthread -I/opt/openmpi-2.0.1/lib -Wl,-rpath -Wl,/opt/openmpi-2.0.1/lib

[OMPI users] Low CPU utilization

Hi, I am running two softwares that use OMPI-2.0.1. Problem is that the CPU utilization is low on the nodes. For example, see the process information below [root@compute-0-1 ~]# ps aux | grep siesta mahmood 14635 0.0 0.0 108156 1300 ?S21:58 0:00 /bin/bash

Re: [OMPI users] -host vs -hostfile

as been deprecated in favor of the > wonderful syntax: > > --map-by ppr:1:node > > > > Or you could change your hostfile to: > > cluster slots=1 > > compute-0-0 slots=1 > > > > > > -Tom > > > > *From:* users [mailto:users-boun...@lists.

Re: [OMPI users] -host vs -hostfile

gt; > On Jul 31, 2017, at 10:00 AM, Mahmood Naderan <mahmood...@gmail.com> > wrote: > > OK. The next question is how touse it with torque (PBS)? currently we > write this directive > > Nodes=1:ppn=2 > > which means 4 threads. Then we omit -np and -hostfile in the m

[OMPI users] -host vs -hostfile

Hi, I have stuck at a problem which I don't remember that on previous versions. when I run a test program with -host, it works. I mean, the process spans to the hosts I specified. However, when I specify -hostfile, it doesn't work!! mahmood@cluster:mpitest$

[OMPI users] test

Regards, Mahmood ___ users mailing list users@lists.open-mpi.org https://rfd.newmexicoconsortium.org/mailman/listinfo/users

[OMPI users] Test, Am I subscribed?

Hello, Regards, Mahmood ___ users mailing list users@lists.open-mpi.org https://rfd.newmexicoconsortium.org/mailman/listinfo/users

Re: [OMPI users] -host vs -hostfile

Well it is confusing!! As you can see, I added four nodes to the host file (the same nodes are used by PBS). The --map-by ppr:1:node works well. However, the PBS directive doesn't work mahmood@cluster:mpitest$ /share/apps/computer/openmpi-2.0.1/bin/mpirun -hostfile hosts --map-by ppr:1:node a.out

Re: [OMPI users] -host vs -hostfile

t; to see if all nodes are listed. > > 4) Run "hostname" with mpirun in a short Torque script: > > #PBS -l nodes=4:ppn=1 > ... > mpirun hostname > > The output should show all four nodes. > > Good luck! > Gus Correa > > On 07/31/2017 02:41 PM, Mahm

Re: [OMPI users] mpif90 unable to find ibverbs

>In short, "mpicc -Wl,-rpath=/my/lib/path helloworld.c -o hello", will >compile a dynamic binary "hello" with built in search path >to "/my/lib/path". Excuse me... Is that a path or file? I get this: mpif90 -g -pthread -Wl,rpath=/share/apps/computer/OpenBLAS-0.2.18 -o iotk_print_kinds.x

Re: [OMPI users] mpif90 unable to find ibverbs

So it seems that -rpath is not available with 1.4 which is ompi came with rocks 6. Regards, Mahmood On Thu, Sep 14, 2017 at 2:44 PM, Mahmood Naderan <mahmood...@gmail.com> wrote: > Well that may be good if someone intend to rebuild ompi. > Lets say, there is an ompi o

Re: [OMPI users] mpif90 unable to find ibverbs

I with --mpirun-prefix-by-default > this will automagically add rpath to the libs. > > Cheers, > > Gilles > > On Thu, Sep 14, 2017 at 6:43 PM, Peter Kjellström <c...@nsc.liu.se> wrote: > > On Wed, 13 Sep 2017 20:13:54 +0430 > > Mahmood Naderan <mahmood...@gmail.c

Re: [OMPI users] mpif90 unable to find ibverbs

>are you sure you are using Open MPI ? I am using the openmpi shipped with Rocks 6 and trying to build Quantum ESPRESSO 6.1 >Beware: static linking is not for the meek. Agree! I found that I have to install compat-dapl-static.x86_64. As can be seen from the name, it is a compatibility library.

Re: [OMPI users] mpif90 unable to find ibverbs

Fortunately Rocks 7 beta is released. So, there is a hope that newer version will be born one day. >https://github.com/sdsc/mpi-roll I wasn't aware of that. Thanks for sharing it. >there is a typo, it should be >-Wl,-rpath,/.../ Thanks a lot. It is now

[OMPI users] mpif90 unable to find ibverbs

Hi, I am trying to build an application with static linking that uses openmpi. in the middle of the build, I get this mpif90 -g -pthread -static -o iotk_print_kinds.x iotk_print_kinds.o libiotk.a /usr/bin/ld: cannot find -libverbs collect2: ld returned 1 exit status However, such library exists

Re: [OMPI users] mpif90 unable to find ibverbs

Thanks Gilles... That has been solved. Another issue is mpif90 -g -pthread -static -o iotk_print_kinds.x iotk_print_kinds.o libiotk.a /usr/bin/ld: cannot find -ldat The name is actually hard to google! I cannot find the library name for "dat". Have you heard of that? There is not "libdat"

Re: [OMPI users] About my GPU performance using Openmpi-2.0.4

>Currently I am using two Tesla K40m cards for my computational work on >quantum espresso (QE) suit http://www.quantum-espresso.org/. My GPU >enabled QE code running very slower than normal version Hi, When I hear such words, I would say, yeah it is quite natural! My personal experience with a

[OMPI users] --oversubscribe option

Hi, On a Ryzen 1800x which has 8 cores and 16 threads, when I run "mpirun -np 16 lammps..." I get an error that there is not enough slot. It seems that --oversubscribe option will fix that. Odd thing is that when I run "mpirun -np 8 lammps" it takes about 46 minutes to complete the job while with

[OMPI users] MPI test program

Hi, Is there any small benchmark for performance measurements? I mean a test which utilize the number of cpus given to the mp ​i for comparison. I want to compare two kernel versions on one system only and not across different platforms. I know Intel MPI benchmark, but I would like to know if

[OMPI users] openmpi with htcondor

Hi, Has anyone here used htcondor scheduler with mpi jobs? I followed the example, openmpiscript, in the condor folder like this [mahmood@rocks7 ~]$ cat mpi.ht universe = parallel executable = openmpiscript arguments = mpihello log = hellompi.log output = hellompi.out error = hellompi.err

[OMPI users] NAS benchmark

Hi, Any body has tried NAS benchmark with ompi? I get the following linker error while building one of the benchmarks. [mahmood@rocks7 NPB3.3-MPI]$ make BT NPROCS=4 CLASS=D = = NAS Parallel Benchmarks 3.3 = = MPI/F77/C

Re: [OMPI users] NAS benchmark

edium" to the compile flags. I'm surprised NAS > Benchmarks need it, though. > > On Sat, Feb 3, 2018 at 3:48 AM, Mahmood Naderan <mahmood...@gmail.com> > wrote: > >> Hi, >> Any body has tried NAS benchmark with ompi? I get the following linker >> error

[OMPI users] mpi and gromacs

Hi Although not directly related to ompi, I would like to know if anybody uses gromcas with mpi support? The binary is gmx_mpi and it has some options for threading. However, I am also able to run that by using running mpirun before gmx_mpi. So, it is possible to run gmx_mpi and mpirun

[OMPI users] libopen-pal not found

Hi, After a successful installation of opmi v3 with cuda enabled, I see that ldd can not find a right lib file although it exists. /usr/local/lib is one of the default locations for the library files. Isn't that? $ which mpic++ /usr/local/bin/mpic++ $ ldd /usr/local/bin/mpic++

[OMPI users] MPI_INIT failed 4.0.1

Hi, After successful installation of v4 on a custom location, I see some errors while the default installation (v2) hasn't. $ /share/apps/softwares/openmpi-4.0.1/bin/mpirun --version mpirun (Open MPI) 4.0.1 Report bugs to http://www.open-mpi.org/community/help/ $

[OMPI users] job termination

Hi, A QuantumEspresso, multinode and multiprocess MPI job has been terminated with the following messages in the log file total cpu time spent up to now is63540.4 secs total energy = -14004.61932175 Ry Harris-Foulkes estimate = -14004.73511665 Ry

Re: [OMPI users] MPI_INIT failed 4.0.1

Thanks for the hint. Regards, Mahmood On Thu, Apr 18, 2019 at 2:47 AM Reuti wrote: > Hi, > > Am 17.04.2019 um 11:07 schrieb Mahmood Naderan: > > > Hi, > > After successful installation of v4 on a custom location, I see some > errors while the default installati