April 2015 - discuss - mailman3.cels.anl.gov

Re: [mpich-discuss] libmpich.so.10: cannot open shared object file
by Kenneth Raffenetti 28 Apr '15

28 Apr '15

Can you confirm your MPICH installation working correctly? Have you tried compiling and running the cpi.c program from the examples directory from the tarball? The MPICH 3.0.4 installation should contain a libmpich.so.10 file, so it will be helpful to know things are installed and working well. Ken On 04/28/2015 04:58 PM, Jorge Pachon wrote: > Hi all, > > I´m trying to run WRF for which I´m using mpich libraries. I recently > installed mpich-3.0.4 and mpich-3.1.4 (with ifort) hoping to install the > libmpich.so.10 file, but neither of them have it ,and I always got this > error > > ./real.exe: error while loading shared libraries: libmpich.so.10: cannot > open shared object file: No such file or directory > > I searched in the mpich folders: /usr/local/lib and > /usr/local/bin/mpich, but cannot find the file > > any help will be appreciated > > Jorge > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

1 0

Re: [mpich-discuss] libmpich.so.10: cannot open shared object file
by Jorge Pachon 28 Apr '15

28 Apr '15

No Junchao, I´m using a WRF already compiled. Should I compile WRF again? thanks On Tue, Apr 28, 2015 at 5:19 PM, Junchao Zhang <jczhang(a)mcs.anl.gov> wrote: > Is your WRF compiled by the mpich you installed? > > --Junchao Zhang > > On Tue, Apr 28, 2015 at 4:58 PM, Jorge Pachon <jpachon3(a)gmail.com> wrote: > >> Hi all, >> >> I´m trying to run WRF for which I´m using mpich libraries. I recently >> installed mpich-3.0.4 and mpich-3.1.4 (with ifort) hoping to install the >> libmpich.so.10 file, but neither of them have it ,and I always got this >> error >> >> ./real.exe: error while loading shared libraries: libmpich.so.10: cannot >> open shared object file: No such file or directory >> >> I searched in the mpich folders: /usr/local/lib and /usr/local/bin/mpich, >> but cannot find the file >> >> any help will be appreciated >> >> Jorge >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

1 0

Re: [mpich-discuss] libmpich.so.10: cannot open shared object file
by Junchao Zhang 28 Apr '15

28 Apr '15

Is your WRF compiled by the mpich you installed? --Junchao Zhang On Tue, Apr 28, 2015 at 4:58 PM, Jorge Pachon <jpachon3(a)gmail.com> wrote: > Hi all, > > I´m trying to run WRF for which I´m using mpich libraries. I recently > installed mpich-3.0.4 and mpich-3.1.4 (with ifort) hoping to install the > libmpich.so.10 file, but neither of them have it ,and I always got this > error > > ./real.exe: error while loading shared libraries: libmpich.so.10: cannot > open shared object file: No such file or directory > > I searched in the mpich folders: /usr/local/lib and /usr/local/bin/mpich, > but cannot find the file > > any help will be appreciated > > Jorge > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

1 0

libmpich.so.10: cannot open shared object file
by Jorge Pachon 28 Apr '15

28 Apr '15

Hi all, I´m trying to run WRF for which I´m using mpich libraries. I recently installed mpich-3.0.4 and mpich-3.1.4 (with ifort) hoping to install the libmpich.so.10 file, but neither of them have it ,and I always got this error ./real.exe: error while loading shared libraries: libmpich.so.10: cannot open shared object file: No such file or directory I searched in the mpich folders: /usr/local/lib and /usr/local/bin/mpich, but cannot find the file any help will be appreciated Jorge _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

1 0

Re: [mpich-discuss] MPICH 3.2b2 packages for Ubuntu, Debian and Slackware (x86 and amd64)
by Huiwei Lu 27 Apr '15

27 Apr '15

Unfortunately, due to the lack of developer resources, MPICH is not supported on Windows anymore including Cygwin. https://wiki.mpich.org/mpich/index.php/FAQ#Q:_Why_can.27t_I_build_MPICH_on_… -- Huiwei On Mon, Apr 27, 2015 at 8:43 AM, Leo Kameni <maxlk.2010(a)my.bristol.ac.uk> wrote: > Can we use it on windows now under cygwin at all? > > On Mon, Apr 27, 2015 at 2:42 PM, Huiwei Lu <huiweilu(a)mcs.anl.gov> wrote: > >> Hi Marcelo, >> >> Thanks for your contribution to MPICH! It makes MPICH better and easier >> to use. We have included your contribution in MPICH download page. >> >> -- >> Huiwei Lu >> Postdoc Appointee >> Mathematics and Computer Science Division >> Argonne National Laboratory >> http://www.mcs.anl.gov/~huiweilu/ >> >> On Fri, Apr 24, 2015 at 2:26 PM, Marcelo Soares Souza < >> marcelo(a)cebacad.net> wrote: >> >>> mpich-3.2b2 packages >>> >>> * Ubuntu 14.10 >>> >>> - amd64 >>> >>> http://www.cebacad.net/files/mpich/ubuntu/mpich-3.2b2/mpich_3.2b2-1ubuntu_a… >>> >>> - x86 >>> >>> http://www.cebacad.net/files/mpich/ubuntu/mpich-3.2b2/mpich_3.2b2-1ubuntu_i… >>> >>> * Debian 8.0 (Jessie) >>> >>> - amd64 >>> >>> http://www.cebacad.net/files/mpich/debian/mpich-3.2b2/mpich_3.2b2-1debian_a… >>> >>> - x86 >>> >>> http://www.cebacad.net/files/mpich/debian/mpich-3.2b2/mpich_3.2b2-1debian_i… >>> >>> * Slackware 14.1 >>> >>> - amd64 >>> >>> http://www.cebacad.net/files/mpich/slackware/mpich-3.2b2/mpich-3.2b2-x86_64… >>> >>> - x86 >>> >>> http://www.cebacad.net/files/mpich/slackware/mpich-3.2b2/mpich-3.2b2-i486-g… >>> >>> Enjoy! >>> >>> -- >>> Marcelo Soares Souza >>> https://marcelo.juntadados.org >>> _______________________________________________ >>> discuss mailing list discuss(a)mpich.org >>> To manage subscription options or unsubscribe: >>> https://lists.mpich.org/mailman/listinfo/discuss >>> >> >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

1 0

Re: [mpich-discuss] MPICH 3.1.4 builds with ib netmod
by Huiwei Lu 27 Apr '15

27 Apr '15

Hi Martin, Thank you for reporting your use of MPICH to us. If you could send us a simple test case that reproduce the crash in your workload, then we can use it to fix our code and make it better. For the question of 3.2b2, the answer is yes! We have been improving MXM since 3.1.4 (thanks to the contribution of Mellanox). It will be worth trying the new release to see if fixes the crash in your workload. Thanks, -- Huiwei Lu Postdoc Appointee Mathematics and Computer Science Division Argonne National Laboratory http://www.mcs.anl.gov/~huiweilu/ On Fri, Apr 24, 2015 at 4:38 PM, Martin Cuma <martin.cuma(a)utah.edu> wrote: > Hello, > > I am getting errors with building -with-device=ch3:nemesis:ib, using GNU, > Intel or PGI compilers, as: > > I am wondering what's going on since this since Intel and GNU worked in > version 3.1.2. I configure as: > ../../../srcdir/mpich/3.1.4/configure --prefix=/uufs/ > chpc.utah.edu/sys/installdir/mpich/3.1.4 --enable-romio > --with-file-system=nfs+ufs --with-mpe -with-device=ch3:nemesis:ib > --enable-threads=runtime --enable-fast=all > > and use RHEL6.6 with stock gcc 4.4.7. > > When I reported a similar issue earlier, Pavan suggested to use MXM - I > tried that and that seems to work, however, perhaps since we run relatively > old OFED (stock RHEL6-like), which does not come with MXM, I used the one > from the latest Mellanox HPC-X, and, I am not sure if that's the best idea > since I see crashes related to communication at certain workloads - which I > don't see with other MPIs or when using the ib netmod in MPICH. > > Would you please also mind commenting on this? Would you expect the just > released 3.2b2 fare better with MXM than the 3.1.4? > > Thanks, > MC > > -- > Martin Cuma > Center for High Performance Computing > Department of Geology and Geophysics > University of Utah > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

1 0

Re: [mpich-discuss] MPICH 3.2b2 packages for Ubuntu, Debian and Slackware (x86 and amd64)
by Leo Kameni 27 Apr '15

27 Apr '15

Can we use it on windows now under cygwin at all? On Mon, Apr 27, 2015 at 2:42 PM, Huiwei Lu <huiweilu(a)mcs.anl.gov> wrote: > Hi Marcelo, > > Thanks for your contribution to MPICH! It makes MPICH better and easier to > use. We have included your contribution in MPICH download page. > > -- > Huiwei Lu > Postdoc Appointee > Mathematics and Computer Science Division > Argonne National Laboratory > http://www.mcs.anl.gov/~huiweilu/ > > On Fri, Apr 24, 2015 at 2:26 PM, Marcelo Soares Souza <marcelo(a)cebacad.net > > wrote: > >> mpich-3.2b2 packages >> >> * Ubuntu 14.10 >> >> - amd64 >> >> http://www.cebacad.net/files/mpich/ubuntu/mpich-3.2b2/mpich_3.2b2-1ubuntu_a… >> >> - x86 >> >> http://www.cebacad.net/files/mpich/ubuntu/mpich-3.2b2/mpich_3.2b2-1ubuntu_i… >> >> * Debian 8.0 (Jessie) >> >> - amd64 >> >> http://www.cebacad.net/files/mpich/debian/mpich-3.2b2/mpich_3.2b2-1debian_a… >> >> - x86 >> >> http://www.cebacad.net/files/mpich/debian/mpich-3.2b2/mpich_3.2b2-1debian_i… >> >> * Slackware 14.1 >> >> - amd64 >> >> http://www.cebacad.net/files/mpich/slackware/mpich-3.2b2/mpich-3.2b2-x86_64… >> >> - x86 >> >> http://www.cebacad.net/files/mpich/slackware/mpich-3.2b2/mpich-3.2b2-i486-g… >> >> Enjoy! >> >> -- >> Marcelo Soares Souza >> https://marcelo.juntadados.org >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

1 0

Re: [mpich-discuss] MPICH 3.2b2 packages for Ubuntu, Debian and Slackware (x86 and amd64)
by Huiwei Lu 27 Apr '15

27 Apr '15

Hi Marcelo, Thanks for your contribution to MPICH! It makes MPICH better and easier to use. We have included your contribution in MPICH download page. -- Huiwei Lu Postdoc Appointee Mathematics and Computer Science Division Argonne National Laboratory http://www.mcs.anl.gov/~huiweilu/ On Fri, Apr 24, 2015 at 2:26 PM, Marcelo Soares Souza <marcelo(a)cebacad.net> wrote: > mpich-3.2b2 packages > > * Ubuntu 14.10 > > - amd64 > > http://www.cebacad.net/files/mpich/ubuntu/mpich-3.2b2/mpich_3.2b2-1ubuntu_a… > > - x86 > > http://www.cebacad.net/files/mpich/ubuntu/mpich-3.2b2/mpich_3.2b2-1ubuntu_i… > > * Debian 8.0 (Jessie) > > - amd64 > > http://www.cebacad.net/files/mpich/debian/mpich-3.2b2/mpich_3.2b2-1debian_a… > > - x86 > > http://www.cebacad.net/files/mpich/debian/mpich-3.2b2/mpich_3.2b2-1debian_i… > > * Slackware 14.1 > > - amd64 > > http://www.cebacad.net/files/mpich/slackware/mpich-3.2b2/mpich-3.2b2-x86_64… > > - x86 > > http://www.cebacad.net/files/mpich/slackware/mpich-3.2b2/mpich-3.2b2-i486-g… > > Enjoy! > > -- > Marcelo Soares Souza > https://marcelo.juntadados.org > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

1 0

Re: [mpich-discuss] Avoiding using two buffers in a non-blocking send receive
by Balaji, Pavan 25 Apr '15

25 Apr '15

We use the mailing list for MPICH-related questions, not general MPI questions. With respect to discuss(a)mpich.org<mailto:[email protected]>, I get those emails and the list has more people who might be able to help you as well. Cc’ed the list. Please send MPICH-related emails to that list. Please send general “how do I write an MPI program” sort of questions to stack overflow or equivalent. I’ll respond to your email this time, but please avoid sending us general MPI questions in the future. I’m not sure what you mean by using a single buffer. Do you mean that, once you send the data to your “send_to" neighbor, you don’t need that buffer anymore and would like to overwrite that with the data coming in from the “recv_from” neighbor? Assuming that’s what you are looking for, there’s no good function to directly do what you are asking for. However, pipelining the data transfer might help the memory usage problem. Specifically, don’t allocate a full receive buffer, but a smaller buffer for a part of the array. Once you receive the data and the corresponding data in your local array is full, you can overwrite it from the receive buffer. Something like this: #define CHUNK_SIZE (1024) #define TOTAL_ARRAY_SIZE (CHUNK_SIZE * SOME_LARGE_NUMBER) struct foobar main_buffer[TOTAL_ARRAY_SIZE]; struct foobar temp_buffer[CHUNK_SIZE]; MPI_Request req[CHUNK_SIZE * 2]; for (j = 0; j < SOME_LARGE_NUMBER; j++) { for (i = 0; i < CHUNK_SIZE; i++) { Isend(… data from main buffer …, &req[2 * i]); Irecv(… data into temp buffer …, &req[2 * i + 1]); } WAITALL(…) memcpy(&main_buffer[j * CHUNK_SIZE], &temp_buffer, …); } You can make this a little better by not waiting for all chunks, but testing any of the chunks to complete and pipelining the copy as well. — Pavan On Apr 25, 2015, at 5:44 PM, Params <praman1(a)ucsc.edu<mailto:[email protected]>> wrote: Hi Pavan, Sorry for directly emailing you about this, but I am a new user to the mpich2 forums and I was not sure if my message to the mailing group reached you (please let me know about that too in case I need to use the forum again). I have a question about mpich usage and would be great if any of you guys could help me out. I have a use-case where I need to transmit an Array of Structures (AoS) among a group of processors in a circular ("ring") fashion. I do that currently by using a non-blocking send and receive, and using two auxiliary buffers on the senders and receivers side respectively. Since the data I am transferring is extremely huge (~60 gb before partitioning), allocating two buffers seems inefficient to me. My question is -- Is there a better way to do it by avoiding "two buffers"? (Perhaps just using one buffer in some way?). Roughly my communication procedure looks like this: //Pack AoS into send buffer (which is a vector<char>) char *msg_ptr = &(msg_send_buf_.front()); for (auto& param : local_primal_params_) { param.pack_to(msg_ptr); msg_ptr += PARAM_BYTENUM; } //Perform non-blocking send receive { MPI_Request send_request; MPI_Status send_stat, recv_stat; MPI_Isend(&(msg_send_buf_.front()), local_primal_params_.size() * PARAM_BYTENUM, MPI_CHAR, send_to, 0, MPI_COMM_WORLD, &send_request); MPI_Recv(&(msg_recv_buf_.front()), local_primal_params_.size() * PARAM_BYTENUM, MPI_CHAR, recv_from, 0, MPI_COMM_WORLD, &recv_stat); MPI_Wait(&send_request, &send_stat); } //Unpack receive buffer back into AoS on receiver side { char *msg_ptr = &(msg_recv_buf_.front()); for (auto& param : local_primal_params_) { param.unpack_from(msg_ptr); msg_ptr += PARAM_BYTENUM; } } Any recommendations will be very helpful. Thanks, Parameswaran Raman PhD Student, UC Santa Cruz

1 0

Avoiding using two buffers in a non-blocking send receive
by Params 25 Apr '15

25 Apr '15

Hello, I have a use-case where I need to transmit an Array of Structures (AoS) among a group of processors in a circular ("ring") fashion. I do that currently by using a non-blocking send and receive, and using two auxiliary buffers on the senders and receivers side respectively. Since the data I am transferring is extremely huge (~60 gb before partitioning), allocating two buffers seems inefficient to me. My question is -- Is there a better way to do it by avoiding "two buffers"? (Perhaps just using one buffer in some way?). Roughly my communication procedure looks like this: //Pack AoS into send buffer (which is a vector<char>) char *msg_ptr = &(msg_send_buf_.front()); for (auto& param : local_primal_params_) { param.pack_to(msg_ptr); msg_ptr += PARAM_BYTENUM; } //Perform non-blocking send receive { MPI_Request send_request; MPI_Status send_stat, recv_stat; MPI_Isend(&(msg_send_buf_.front()), local_primal_params_.size() * PARAM_BYTENUM, MPI_CHAR, send_to, 0, MPI_COMM_WORLD, &send_request); MPI_Recv(&(msg_recv_buf_.front()), local_primal_params_.size() * PARAM_BYTENUM, MPI_CHAR, recv_from, 0, MPI_COMM_WORLD, &recv_stat); MPI_Wait(&send_request, &send_stat); } //Unpack receive buffer back into AoS on receiver side { char *msg_ptr = &(msg_recv_buf_.front()); for (auto& param : local_primal_params_) { param.unpack_from(msg_ptr); msg_ptr += PARAM_BYTENUM; } } Any recommendations will be very helpful. -- Thanks, params http://people.ucsc.edu/~praman1/ _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

1 0