March 2018 - discuss - mailman3.cels.anl.gov

Re: [mpich-discuss] Missing instructions
by Kenneth Raffenetti 15 Mar '18

15 Mar '18

I updated this section to include a command to retrieve the needed submodules. https://wiki.mpich.org/mpich/index.php/Getting_And_Building_MPICH#Setting_u… Ken On 03/15/2018 07:49 AM, William Gropp wrote: > When I run autogen.sh, I get: > > gropp$ ./autogen.sh > > #################################### > ## Checking user environment > #################################### > > Verifying the location of autogen.sh... done > Checking if autotools are in the same location... yes, all in /Users/gropp > Checking for autoconf version... >= 2.67 > Checking for automake version... >= 1.15 > Checking for libtool version... >= 2.4.4 > Checking for UNIX find... done > Checking if xargs rm -rf works... yes > > ########################################################### > ## Checking submodules > ########################################################### > > ===> ERROR: Submodule src/hwloc is not checked out > wdg-macbook:mpich-trunk gropp$ > > How exactly is src/hwloc to be checked out? There is nothing about that > at https://wiki.mpich.org/mpich/index.php/Getting_And_Building_MPICH . > Are up-to-date instructions available? > > Bill > > William Gropp > Director and Chief Scientist, NCSA > Thomas M. Siebel Chair in Computer Science > University of Illinois Urbana-Champaign > > > > > > > > > _______________________________________________ > 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

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missing mpi_f08 module in MPICH 3.2
by Damian Rouson 15 Mar '18

15 Mar '18

According to the MPICH Changes web page, "Fortran 2008 bindings are enabled by default and fully supported” starting in MPICH 3.2. Could someone please point me to documentation on using the bindings? My installation of MPICH 3.2 doesn’t find the mpi_f08 module described in MPI 3.1 standard. My draft copy of the standard states the following at the beginning of Section 17.1.2: "An MPI implementation providing a Fortran interface must provide a module named mpi_f08 that can be used in a Fortran program.” Below is an example of what I’m seeing. Damian $ cat use_mpi_f08.f90 program main use mpi_f08 implicit none end program $ mpifort use_mpi_f08.f90 use_mpi_f08.f90:2:6: use mpi_f08 1 Fatal Error: Can't open module file ‘mpi_f08.mod’ for reading at (1): No such file or directory compilation terminated. $ mpiexec --version HYDRA build details: Version: 3.2 Release Date: Wed Nov 11 22:06:48 CST 2015 CC: gcc CXX: g++ F77: gfortran F90: gfortran Configure options: '--disable-option-checking' '--prefix=/opt/mpich/3.2/gnu/7.2.0' 'CC=gcc' 'CXX=g++' 'FC=gfortran' '--cache-file=/dev/null' '--srcdir=/home/rouson/Desktop/Builds/opencoarrays/prerequisites/downloads/mpich-3.2/src/pm/hydra' 'CFLAGS= -O2' 'LDFLAGS=' 'LIBS=-lpthread ' 'CPPFLAGS= -I/home/rouson/Desktop/Builds/opencoarrays/prerequisites/builds/mpich-3.2/src/mpl/include -I/home/rouson/Desktop/Builds/opencoarrays/prerequisites/downloads/mpich-3.2/src/mpl/include -I/home/rouson/Desktop/Builds/opencoarrays/prerequisites/downloads/mpich-3.2/src/openpa/src -I/home/rouson/Desktop/Builds/opencoarrays/prerequisites/builds/mpich-3.2/src/openpa/src -D_REENTRANT -I/home/rouson/Desktop/Builds/opencoarrays/prerequisites/builds/mpich-3.2/src/mpi/romio/include' Process Manager: pmi Launchers available: ssh rsh fork slurm ll lsf sge manual persist Topology libraries available: hwloc Resource management kernels available: user slurm ll lsf sge pbs cobalt Checkpointing libraries available: blcr Demux engines available: poll select _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] Missing instructions
by Shuwei Zhao 15 Mar '18

15 Mar '18

Hi will, I was confused about this for a while when I was bootstraping the mpich. hwloc is a git submodule inside mpich, you need to separately git clone it into your local client, I remember there are several other submodule as well like src/izem which needs to be treated the same. Thanks, Shuwei On Thu, 15 Mar 2018 at 07:49 William Gropp <wgropp(a)illinois.edu> wrote: > When I run autogen.sh, I get: > > gropp$ ./autogen.sh > > #################################### > ## Checking user environment > #################################### > > Verifying the location of autogen.sh... done > Checking if autotools are in the same location... yes, all in /Users/gropp > Checking for autoconf version... >= 2.67 > Checking for automake version... >= 1.15 > Checking for libtool version... >= 2.4.4 > Checking for UNIX find... done > Checking if xargs rm -rf works... yes > > ########################################################### > ## Checking submodules > ########################################################### > > ===> ERROR: Submodule src/hwloc is not checked out > wdg-macbook:mpich-trunk gropp$ > > How exactly is src/hwloc to be checked out? There is nothing about that > at https://wiki.mpich.org/mpich/index.php/Getting_And_Building_MPICH . > Are up-to-date instructions available? > > Bill > > William Gropp > Director and Chief Scientist, NCSA > Thomas M. Siebel Chair in Computer Science > University of Illinois Urbana-Champaign > > > > > > > _______________________________________________ > 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

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Missing instructions
by William Gropp 15 Mar '18

15 Mar '18

When I run autogen.sh, I get: gropp$ ./autogen.sh #################################### ## Checking user environment #################################### Verifying the location of autogen.sh... done Checking if autotools are in the same location... yes, all in /Users/gropp Checking for autoconf version... >= 2.67 Checking for automake version... >= 1.15 Checking for libtool version... >= 2.4.4 Checking for UNIX find... done Checking if xargs rm -rf works... yes ########################################################### ## Checking submodules ########################################################### ===> ERROR: Submodule src/hwloc is not checked out wdg-macbook:mpich-trunk gropp$ How exactly is src/hwloc to be checked out? There is nothing about that at https://wiki.mpich.org/mpich/index.php/Getting_And_Building_MPICH . Are up-to-date instructions available? Bill William Gropp Director and Chief Scientist, NCSA Thomas M. Siebel Chair in Computer Science University of Illinois Urbana-Champaign _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Bug in autogen.sh selects wrong version of libtoolize and gives bogus error message
by William Gropp 14 Mar '18

14 Mar '18

This code is incorrect if test -z "${LIBTOOLIZE+set}" && ( glibtoolize --version ) >/dev/null 2>&1 ; then libtoolize=glibtoolize else libtoolize=${LIBTOOLIZE:-libtoolize} fi because it selects glibtoolsize over libtoolize, even if autoconf etc. have been installed by the user (me in this case) ahead of the ones defined by the operating system (MacOS in my case). Even worse, it then tells me: Checking if autotools are in the same location... no autoconf is in /Users/gropp automake is in /Users/gropp libtool is in /opt/local But here’s what I get: wdg-macbook: gropp$ which autoconf /Users/gropp/bin/autoconf wdg-macbook: gropp$ which automake /Users/gropp/bin/automake wdg-macbook: gropp$ which libtool /Users/gropp/bin/libtool wdg-macbook: gropp$ So: autogen.sh claims the libtool in the path is in /opt/local , which it is not, and autogen.sh claims that the tools are in directories that they are not in (it always dropped “bin” - there is no requirement that the directory path end in bin. I can work around these errors by setting LIBTOOLIZE, but I should not need to do that and I had to debug autogen.sh to discover what it really wanted. Bill William Gropp Director and Chief Scientist, NCSA Thomas M. Siebel Chair in Computer Science University of Illinois Urbana-Champaign _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Is mpich/master:a8a2b30fd21 tested with Petsc?
by Eric Chamberland 13 Mar '18

13 Mar '18

Hi, each night we are testing mpich/master with our petsc-based code. I don't know if PETSc team is doing the same thing with mpich/master? (Maybe it is a good idea?) Everything was fine (except the issue https://github.com/pmodels/mpich/issues/2892) up to commit 7b8d64debd, but since commit mpich:a8a2b30fd21), I have a segfault on a any parallel nightly test. For example, a 2 process test ends at almost different execution points: rank 0: #003: /lib64/libpthread.so.0(+0xf870) [0x7f25bf908870] #004: /pmi/cmpbib/compilation_BIB_dernier_mpich/COMPILE_AUTO/BIB/bin/BIBMEFGD.opt() [0x64a788] #005: /lib64/libc.so.6(+0x35140) [0x7f25bca18140] #006: /lib64/libc.so.6(__poll+0x2d) [0x7f25bcabfbfd] #007: /opt/mpich-3.x_debug/lib/libmpi.so.0(+0x1e4cc9) [0x7f25bd90ccc9] #008: /opt/mpich-3.x_debug/lib/libmpi.so.0(+0x1ea55c) [0x7f25bd91255c] #009: /opt/mpich-3.x_debug/lib/libmpi.so.0(+0xba657) [0x7f25bd7e2657] #010: /opt/mpich-3.x_debug/lib/libmpi.so.0(PMPI_Waitall+0xe3) [0x7f25bd7e3343] #011: /opt/petsc-3.8.3_debug_mpich-3.x_debug/lib/libpetsc.so.3.8(PetscGatherMessageLengths+0x654) [0x7f25c4bb3193] #012: /opt/petsc-3.8.3_debug_mpich-3.x_debug/lib/libpetsc.so.3.8(VecScatterCreate_PtoS+0x859) [0x7f25c4e82d7f] #013: /opt/petsc-3.8.3_debug_mpich-3.x_debug/lib/libpetsc.so.3.8(VecScatterCreate+0x5684) [0x7f25c4e4d055] #014: /opt/petsc-3.8.3_debug_mpich-3.x_debug/lib/libpetsc.so.3.8(VecCreateGhostWithArray+0x688) [0x7f25c4e01a39] #015: /opt/petsc-3.8.3_debug_mpich-3.x_debug/lib/libpetsc.so.3.8(VecCreateGhost+0x179) [0x7f25c4e020f6] rank 1: #002: /pmi/cmpbib/compilation_BIB_dernier_mpich/COMPILE_AUTO/GIREF/lib/libgiref_opt_Util.so(traitementSignal+0x2bd0) [0x7f62df8e7310] #003: /lib64/libc.so.6(+0x35140) [0x7f62d3bc9140] #004: /lib64/libc.so.6(__poll+0x2d) [0x7f62d3c70bfd] #005: /opt/mpich-3.x_debug/lib/libmpi.so.0(+0x1e4cc9) [0x7f62d4abdcc9] #006: /opt/mpich-3.x_debug/lib/libmpi.so.0(+0x1ea55c) [0x7f62d4ac355c] #007: /opt/mpich-3.x_debug/lib/libmpi.so.0(+0x12c9c5) [0x7f62d4a059c5] #008: /opt/mpich-3.x_debug/lib/libmpi.so.0(+0x12e102) [0x7f62d4a07102] #009: /opt/mpich-3.x_debug/lib/libmpi.so.0(+0xf17a1) [0x7f62d49ca7a1] #010: /opt/mpich-3.x_debug/lib/libmpi.so.0(+0x3facf) [0x7f62d4918acf] #011: /opt/mpich-3.x_debug/lib/libmpi.so.0(+0x3fc3d) [0x7f62d4918c3d] #012: /opt/mpich-3.x_debug/lib/libmpi.so.0(+0xf18d8) [0x7f62d49ca8d8] #013: /opt/mpich-3.x_debug/lib/libmpi.so.0(+0x3fb88) [0x7f62d4918b88] #014: /opt/mpich-3.x_debug/lib/libmpi.so.0(+0x3fc3d) [0x7f62d4918c3d] #015: /opt/mpich-3.x_debug/lib/libmpi.so.0(MPI_Barrier+0x27b) [0x7f62d4918edb] #016: /opt/petsc-3.8.3_debug_mpich-3.x_debug/lib/libpetsc.so.3.8(PetscCommGetNewTag+0x3ff) [0x7f62dbceb055] #017: /opt/petsc-3.8.3_debug_mpich-3.x_debug/lib/libpetsc.so.3.8(PetscObjectGetNewTag+0x15d) [0x7f62dbceaadb] #018: /opt/petsc-3.8.3_debug_mpich-3.x_debug/lib/libpetsc.so.3.8(VecScatterCreateCommon_PtoS+0x1ee) [0x7f62dc03625c] #019: /opt/petsc-3.8.3_debug_mpich-3.x_debug/lib/libpetsc.so.3.8(VecScatterCreate_PtoS+0x29c4) [0x7f62dc035eea] #020: /opt/petsc-3.8.3_debug_mpich-3.x_debug/lib/libpetsc.so.3.8(VecScatterCreate+0x5684) [0x7f62dbffe055] #021: /opt/petsc-3.8.3_debug_mpich-3.x_debug/lib/libpetsc.so.3.8(VecCreateGhostWithArray+0x688) [0x7f62dbfb2a39] #022: /opt/petsc-3.8.3_debug_mpich-3.x_debug/lib/libpetsc.so.3.8(VecCreateGhost+0x179) [0x7f62dbfb30f6] Have some other users (PETSc users?) reported problem? Thanks, Eric ps: usual informations: mpich logs: http://www.giref.ulaval.ca/~cmpgiref/dernier_mpich/2018.03.12.05h39m54s_con… http://www.giref.ulaval.ca/~cmpgiref/dernier_mpich/2018.03.12.05h39m54s_con… http://www.giref.ulaval.ca/~cmpgiref/dernier_mpich/2018.03.12.05h39m54s_mpi… http://www.giref.ulaval.ca/~cmpgiref/dernier_mpich/2018.03.12.05h39m54s_c.t… http://www.giref.ulaval.ca/~cmpgiref/dernier_mpich/2018.03.12.05h39m54s_m.t… http://www.giref.ulaval.ca/~cmpgiref/dernier_mpich/2018.03.12.05h39m54s_mi.… http://www.giref.ulaval.ca/~cmpgiref/dernier_mpich/2018.03.12.05h39m54s_ope… http://www.giref.ulaval.ca/~cmpgiref/dernier_mpich/2018.03.12.05h39m54s_mpl… http://www.giref.ulaval.ca/~cmpgiref/dernier_mpich/2018.03.12.05h39m54s_pm_… http://www.giref.ulaval.ca/~cmpgiref/dernier_mpich/2018.03.12.05h39m54s_pm_… http://www.giref.ulaval.ca/~cmpgiref/dernier_mpich/2018.03.12.05h39m54s_mpi… Petsc logs: http://www.giref.ulaval.ca/~cmpgiref/dernier_mpich/2018.03.12.05h39m54s_con… http://www.giref.ulaval.ca/~cmpgiref/dernier_mpich/2018.03.12.05h39m54s_mak… http://www.giref.ulaval.ca/~cmpgiref/dernier_mpich/2018.03.12.05h39m54s_def… http://www.giref.ulaval.ca/~cmpgiref/dernier_mpich/2018.03.12.05h39m54s_RDi… http://www.giref.ulaval.ca/~cmpgiref/dernier_mpich/2018.03.12.05h39m54s_CMa… _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] error while configuring mpich 3.2
by Kenneth Raffenetti 12 Mar '18

12 Mar '18

Can you contact your system administrators on how to properly select/enable the Intel C++ compiler for your system? This does not appear to be an MPICH problem. Ken On 03/11/2018 06:58 PM, Guido granda muñoz wrote: > Hello, > > I am trying to configure mpich3.2 by source and I get the following error: > > configure: error: C++ compiler icpc has neither iostream nor iostream.h. > configure: error: ./configure failed for test/mpi > > > The configurations options that I used were: > > ./configure --prefix=/fs/posgrado16/other0/guido/libraries/mpich-3.2 > --enable-fortran=yes --enable-cxx > > The test/mpi/config.log, config.log, are attached to this email. Could > you please tell me how to solve this problem and include details because > I am not an expert. > > Kind Regards, > -- > Guido > > > _______________________________________________ > 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

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error while configuring mpich 3.2
by Guido granda muñoz 11 Mar '18

11 Mar '18

Hello, I am trying to configure mpich3.2 by source and I get the following error: configure: error: C++ compiler icpc has neither iostream nor iostream.h. configure: error: ./configure failed for test/mpi The configurations options that I used were: ./configure --prefix=/fs/posgrado16/other0/guido/libraries/mpich-3.2 --enable-fortran=yes --enable-cxx The test/mpi/config.log, config.log, are attached to this email. Could you please tell me how to solve this problem and include details because I am not an expert. Kind Regards, -- Guido _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] Joining a job from a process without mpiexec parent
by Dmitriy Lyubimov 05 Mar '18

05 Mar '18

Mike: exactly. That's about where our conversation ended circa 2 years ago. IIRC I was told along the lines that it was not supported, and i pointed out that MPI standard recommends (if not requires) this way of doing things. I figured 3.3 is now getting closer to release now that i try to see if something has changed for it, but I guess I have to assume the developing parties are not interested in that user experience themselves, so I just have to conclude that nothing unfortunately for me has changed in that regard since 3.2 in terms of UI experience. Which is a shame really, because this is one of the easiest ways for integrating 3rd party process management including 3rd party clouds, containers, resource managers etc. etc. On Sat, Mar 3, 2018 at 2:30 PM, <Michael.Stokes(a)uah.edu> wrote: > Dmitriy, > > I've written a server and client code example and compiled it using MPICH > 3.2 using MPI_Comm_{accept,connect}() to see if MPICH 3.2 will form a > intercommunicator between the two processes without using a launcher > {mpiexec,mpirun}. Before I started, I read the instructions ( MPI Specs > 3.1 section 10.5.2). It states > > "A high-quality implementation will allow any process (including those not > started with a > “parallel application” mechanism) to become an MPI process by calling > MPI_INIT. Such > a process can then connect to other MPI processes using the > MPI_COMM_ACCEPT and > MPI_COMM_CONNECT routines, or spawn other MPI processes. MPI does not > mandate > this behavior, but strongly encourages it where technically feasible." > > Case 1) With the server and client run directly from the command-line the > server executes down to the MPI_Comm_accept() call as anticipated, but when > the port name is entered into the client process, it dies on > MPI_Comm_connect() with the error ... > > match_arg (utils/args/args.c:159): unrecognized argument pmi_args > [mpiexec@Que] HYDU_parse_array (utils/args/args.c:174): argument matching > returned error > [mpiexec@Que] parse_args (ui/mpich/utils.c:1596): error parsing input > array > [mpiexec@Que] HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1648): unable > to parse user arguments > [mpiexec@Que] main (ui/mpich/mpiexec.c:153): error parsing parameters > > Case 2) When I run the server directly from the command-line and launch > the client using mpirun, the same sort of error messages emerge but this > time from the server. Since the server blocks on the accept() call, the > client must be successful in sending something to the server. But > apparently not what it is expecting. > > So my conclusion is that MPICH is attempting to support the Singleton > process, but either has a bug or there might be an installation issue on my > end. > > Hopefully someone can help sort this. > > --Mike > > > _______________________________________________ > 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

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Re: [mpich-discuss] Joining a job from a process without mpiexec parent
by Michael.Stokes＠uah.edu 03 Mar '18

03 Mar '18

Dmitriy, I've written a server and client code example and compiled it using MPICH 3.2 using MPI_Comm_{accept,connect}() to see if MPICH 3.2 will form a intercommunicator between the two processes without using a launcher {mpiexec,mpirun}. Before I started, I read the instructions ( MPI Specs 3.1 section 10.5.2). It states "A high-quality implementation will allow any process (including those not started with a “parallel application” mechanism) to become an MPI process by calling MPI_INIT. Such a process can then connect to other MPI processes using the MPI_COMM_ACCEPT and MPI_COMM_CONNECT routines, or spawn other MPI processes. MPI does not mandate this behavior, but strongly encourages it where technically feasible." Case 1) With the server and client run directly from the command-line the server executes down to the MPI_Comm_accept() call as anticipated, but when the port name is entered into the client process, it dies on MPI_Comm_connect() with the error ... match_arg (utils/args/args.c:159): unrecognized argument pmi_args [mpiexec@Que] HYDU_parse_array (utils/args/args.c:174): argument matching returned error [mpiexec@Que] parse_args (ui/mpich/utils.c:1596): error parsing input array [mpiexec@Que] HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1648): unable to parse user arguments [mpiexec@Que] main (ui/mpich/mpiexec.c:153): error parsing parameters Case 2) When I run the server directly from the command-line and launch the client using mpirun, the same sort of error messages emerge but this time from the server. Since the server blocks on the accept() call, the client must be successful in sending something to the server. But apparently not what it is expecting. So my conclusion is that MPICH is attempting to support the Singleton process, but either has a bug or there might be an installation issue on my end. Hopefully someone can help sort this. --Mike _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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