Re: [OMPI users] PGI 8.0-4 doesn't like ompi/mca/op/op.h
Hi, I am pretty sure that C++ has no restrict keyword (only C99), so IMHO it's not the compilers fault is not compiling. You probably want to turn restricts off for C++ by default, unless you know the compiler supports it. best regards, Samuel smime.p7s Description: S/MIME Cryptographic Signature
Re: [OMPI users] /usr/bin/ld: skipping incompatible /usr/local/lib/libgcc_s.so when searching for -lgcc_s
Hi Gary, that is a linker warning. You probably have a libgcc_s.so in 32 and 64 bit. The linker finds the "wrong" version first and skips it. After that the matching one is linked and thus your program runs. So nothing to worry about. To avoid the warning you can switch the (default) search order. best regards, Samuel Gary Draving wrote: Hi Everyone, I'm getting a "/usr/bin/ld: skipping incompatible /usr/local/lib/libgcc_s.so when searching for -lgcc_s" when compiling some of the openmpi 1.3 examples. The programs still compile and run. Does anyone know if this warning is something I should be concerned about and/or how I can get it resolved. Thanks, Gary [admin@compute-0-39 progs]$ /usr/local/bin/mpicc hello.c -o hello /usr/bin/ld: skipping incompatible /usr/local/lib/libgcc_s.so when searching for -lgcc_s smime.p7s Description: S/MIME Cryptographic Signature
Re: [OMPI users] Performance: MPICH2 vs OpenMPI
Hi, my experience is that OpenMPI has slightly less latency and less bandwidth than Intel MPI (which is based on mpich2) using InfiniBand. I don't remember the numbers using shared memory. As you are seeing a huge difference, I would suspect that either something with your compilation is strange or more probable that you hit the cc-numa effect of the Opteron. You might want to bind the MPI processes (and even clean the filesystem caches) to avoid that effect. best regards, Samuel Sangamesh B wrote: Hi All, I wanted to switch from mpich2/mvapich2 to OpenMPI, as OpenMPI supports both ethernet and infiniband. Before doing that I tested an application 'GROMACS' to compare the performance of MPICH2 & OpenMPI. Both have been compiled with GNU compilers. After this benchmark, I came to know that OpenMPI is slower than MPICH2. This benchmark is run on a AMD dual core, dual opteron processor. Both have compiled with default configurations. The job is run on 2 nodes - 8 cores. OpenMPI - 25 m 39 s. MPICH2 - 15 m 53 s. Any comments ..? Thanks, Sangamesh smime.p7s Description: S/MIME Cryptographic Signature
[OMPI users] Number of file handles limiting the number off processes?
Hi, mpiexec seems to need a file handle per started process. By default the number of file handles is set to 1024 here, thus I can start about 900 something processes. With higher numbers I get mca_oob_tcp_accept: accept() failed: Too many open files (24). If I decrease the file handles on the shell I run mpiexec from, I get the error with less processes. However no MPI process is started on the local machine. The first thing I am wondering about is the TCP because Infiniband is used for communication. And secondly what are the files/connections used for? Do I really have to set the file handles to 5000 (and to 32000 in a few years) for large MPI programs or is there a workaround? Another thing that I don't get is that the problem only arises if I start an MPI program. mpiexec -np 2000 hostname works fine. best regards, Samuel smime.p7s Description: S/MIME Cryptographic Signature
Re: [OMPI users] libibverbs and openmpi 1.2.6
Hi Jeff, This suggests that perhaps 1.2.6 was configured with --enable-static or --disable-dlopen. If either of these two options were used, OMPI will suck all the plugins to become part of libmpi (and friends), and therefore the plugins' dependencies will therefore become dependencies of libmpi (and friends). thanks for the hint. You are right we used --enable-static with 1.2.6. best regards Samuel P.S.: I liked you videos btw. -- Dipl.-Inform. Samuel Sarholz- High Performance Computing, RWTH Aachen University, Center for Computing and Communication, Seffenter Weg 23, 52074 Aachen (Germany), Office: 2.13 Tel: +49 241/80-24915 - Fax: +49 241/80-22134 mailto:sarh...@rz.rwth-aachen.de www.rz.rwth-aachen.de smime.p7s Description: S/MIME Cryptographic Signature
Re: [OMPI users] libibverbs and openmpi 1.2.6
Hi, Nothing changed between 1.2.5 and 1.2.6 with regards to depending on libibverbs. Ok then I need to check what we did differently when installing both versions. The mpicc wrapper from 1.2.6 links -libverbs. (It shows up with mpicc -V). Does ldd show that your apps depend on libibverbs? Yes, ldd shows a dependency. Best regards, Samuel -- Dipl.-Inform. Samuel Sarholz- High Performance Computing, RWTH Aachen University, Center for Computing and Communication, Seffenter Weg 23, 52074 Aachen (Germany), Office: 2.13 Tel: +49 241/80-24915 - Fax: +49 241/80-22134 mailto:sarh...@rz.rwth-aachen.de www.rz.rwth-aachen.de smime.p7s Description: S/MIME Cryptographic Signature
[OMPI users] libibverbs and openmpi 1.2.6
Hi, we have a some issues with the openmpi 1.2.6 and libibverbs. We have some machines with Infiniband and some without. We compiled openmpi with IB support. With OpenMPI 1.2.5 it was no problem running that version on the machines without IB. However with 1.2.6 the library libibverbs is linked which doen't exist on some of the machines. Is there a way to get programs compiled on a IB machine running them on machines without IB? (remove the dependency to libibverbs from openmpi 1.2.6) best regards, Samuel -- Dipl.-Inform. Samuel Sarholz- High Performance Computing, RWTH Aachen University, Center for Computing and Communication, Seffenter Weg 23, 52074 Aachen (Germany), Office: 2.13 Tel: +49 241/80-24915 - Fax: +49 241/80-22134 mailto:sarh...@rz.rwth-aachen.de www.rz.rwth-aachen.de smime.p7s Description: S/MIME Cryptographic Signature
[OMPI users] Communicators in Fortran and C
Hi, I have problems running a Fortran program which is calling a C library with OpenMPI. The problem is that the Fortan part has a communicator which is passed to the C library. And if I understand the headers right a communicator is an integer in fortran, but a struct on the C side of openmpi. Is there a way to translate/cast these communicators? best regards, Samuel smime.p7s Description: S/MIME Cryptographic Signature
