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

Re: [mpich-discuss] datatypes and MPI-3 shared memory windows
by Min Si 10 May '18

10 May '18

Hi Lux, Yes, you can use MPI datatype with shared window. Can you provide more information about the purpose to use shared window thus we can give appropriate suggestion ? Best regards, Min On 2018/05/10 10:05, Luis Cebamanos wrote: > Hi all, > > Is there a way to deal with MPI datatypes when using shmm windows? What > is the advice to convert a flat MPI code that uses MPI datatypes for > halo exchanges to use shmm windows? > > Thanks! > Lux > > > _______________________________________________ > 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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datatypes and MPI-3 shared memory windows
by Luis Cebamanos 10 May '18

10 May '18

Hi all, Is there a way to deal with MPI datatypes when using shmm windows? What is the advice to convert a flat MPI code that uses MPI datatypes for halo exchanges to use shmm windows? Thanks! Lux _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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couldn't built mpich-master on SuSE Linux with Sun C
by Siegmar Gross 09 May '18

09 May '18

Hi, I tried to install mpich-master on my "SUSE Linux Enterprise Server 12.3 (x86_64)" with Sun C 5.15 (Oracle Developer Studio 12.6). Unfortunately, I get the following error. loki mpich-master_2018-05-09_Linux.x86_64.64_cc 143 tail -22 log.make.Linux.x86_64.64_cc | grep -v NOTICE MOD src/binding/fortran/use_mpi/mpi_base.mod-stamp GEN lib/libmpi.la MOD src/binding/fortran/use_mpi/mpi.mod-stamp "./src/include/mpichconf.h", line 1711: Warning (Anachronism): Attempt to redefine __restrict__ without using #undef. 1 Warning(s) detected. f90: Warning: Option -shared passed to ld, if ld is invoked, ignored otherwise f90: Warning: Option --whole-archive passed to ld, if ld is invoked, ignored otherwise f90: Warning: Option --no-whole-archive passed to ld, if ld is invoked, ignored otherwise f90: Warning: Option -path passed to ld, if ld is invoked, ignored otherwise f90: Warning: Option -path passed to ld, if ld is invoked, ignored otherwise f90: Warning: Option -soname passed to ld, if ld is invoked, ignored otherwise /usr/bin/ld: -r and -shared may not be used together postopt: error: ld failed to link the binary Makefile:16751: recipe for target 'lib/libmpi.la' failed make[2]: *** [lib/libmpi.la] Error 2 make[2]: Leaving directory '/export2/src/mpich-master/mpich-master_2018-05-09_Linux.x86_64.64_cc' Makefile:39685: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/export2/src/mpich-master/mpich-master_2018-05-09_Linux.x86_64.64_cc' Makefile:10429: recipe for target 'all' failed make: *** [all] Error 2 loki mpich-master_2018-05-09_Linux.x86_64.64_cc 144 I used the following commands to download and configure MPICH. git clone https://github.com/pmodels/mpich.git cd mpich git submodule update --init --recursive autogen.sh mkdir mpich-master_`date -I'date'`_${SYSTEM_ENV}.${MACHINE_ENV}.64_cc cd mpich-master_`date -I'date'`_${SYSTEM_ENV}.${MACHINE_ENV}.64_cc ../mpich/configure \ --prefix=/usr/local/mpich-master_64_cc \ --libdir=/usr/local/mpich-master_64_cc/lib64 \ --includedir=/usr/local/mpich-master_64_cc/include64 \ CC="cc" CXX="CC" F77="f77" FC="f95" \ CFLAGS="-m64" CXXFLAGS="-m64" FFLAGS="-m64" FCFLAGS="-m64" \ LDFLAGS="-m64 -L/usr/lib64 -R/usr/lib64" \ --enable-fortran=yes --enable-cxx --enable-romio \ --enable-debuginfo --enable-smpcoll \ --enable-threads=multiple --with-thread-package=posix \ --enable-shared \ |& tee log.configure.$SYSTEM_ENV.$MACHINE_ENV.64_cc make -j 6 |& tee log.make.$SYSTEM_ENV.$MACHINE_ENV.64_cc I've also downloaded mpich-master-v3.3b2-49-g1807b26 and I was able to build it with Sun C. loki local 172 ls -l mpich-3.3_64_cc/bin/ mpich-master_64_cc/bin/ mpich-3.3_64_cc/bin/: total 28632 -rwxr-xr-x 1 root root 3479448 May 4 09:23 hydra_nameserver -rwxr-xr-x 1 root root 3473592 May 4 09:23 hydra_persist -rwxr-xr-x 1 root root 3786272 May 4 09:23 hydra_pmi_proxy lrwxrwxrwx 1 root root 6 May 4 09:23 mpic++ -> mpicxx -rwxr-xr-x 1 root root 9588 May 4 09:23 mpicc -rwxr-xr-x 1 root root 6847024 May 4 09:23 mpichversion -rwxr-xr-x 1 root root 9163 May 4 09:23 mpicxx lrwxrwxrwx 1 root root 13 May 4 09:23 mpiexec -> mpiexec.hydra -rwxr-xr-x 1 root root 4635304 May 4 09:23 mpiexec.hydra lrwxrwxrwx 1 root root 13 May 4 09:23 mpirun -> mpiexec.hydra -rwxr-xr-x 1 root root 7053376 May 4 09:23 mpivars -rwxr-xr-x 1 root root 3430 May 4 09:23 parkill mpich-master_64_cc/bin/: total 14864 -rwxr-xr-x 1 root root 3439656 May 9 09:17 hydra_nameserver -rwxr-xr-x 1 root root 3437896 May 9 09:17 hydra_persist -rwxr-xr-x 1 root root 3745912 May 9 09:17 hydra_pmi_proxy lrwxrwxrwx 1 root root 13 May 9 09:17 mpiexec -> mpiexec.hydra -rwxr-xr-x 1 root root 4587736 May 9 09:17 mpiexec.hydra lrwxrwxrwx 1 root root 13 May 9 09:17 mpirun -> mpiexec.hydra loki local 173 mpich-3.3_64_cc/bin/mpichversion MPICH Version: 3.3b2 MPICH Release date: Fri May 4 00:55:55 CDT 2018 MPICH Device: ch3:nemesis MPICH configure: --prefix=/usr/local/mpich-3.3_64_cc --libdir=/usr/local/mpich-3.3_64_cc/lib64 --includedir=/usr/local/mpich-3.3_64_cc/include64 CC=cc CXX=CC F77=f77 FC=f95 CFLAGS=-m64 CXXFLAGS=-m64 FFLAGS=-m64 FCFLAGS=-m64 LDFLAGS=-m64 -L/usr/lib64 -R/usr/lib64 --enable-fortran=ye --enable-cxx --enable-romio --enable-debuginfo --enable-smpcoll --enable-threads=multiple --with-thread-package=posix --enable-shared MPICH CC: cc -m64 -O2 MPICH CXX: CC -m64 -O2 MPICH F77: f77 -m64 MPICH FC: f95 -m64 MPICH Custom Information: loki local 174 Do you have any ideas what's going wrong with the master version? I would be grateful, if somebody can fix the problem. Do you need anything else? Thank you very much for any help in advance. Kind regards Siegmar _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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mpich-3.2.1 install fail (on Ubuntu 16.04)
by Jan Marek Szubert 04 May '18

04 May '18

make fais when : tries to open a non-existent dir on /tmp/ I have spent a few days trying to determine the reason for the failure. If anything should be clear from the attached log files I would appreciate the heads up. The config.log file is nearly half a megabyte, otherwise, I would have included it also. I am still wading through the strace output, but it is rather overwhelming. gcc (Ubuntu 5.4.0-6ubuntu1~16.04.9) 5.4.0 20160609 configure and make output files attached. CC src/util/other/lib_libmpi_la-assert.lo *( cd . && ./maint/extractcvars --dirs="`cat ./maint/cvardirs`")* Error: open directory /tmp/_HMuTRgPPE/mpich-3.2.1/maint/../src/mpi -- No such file or directory Makefile:39284: recipe for target 'src/util/cvar/mpich_cvars.c' failed make[2]: *** [src/util/cvar/mpich_cvars.c] Error 2 make[2]: Leaving directory '/home/jan/amber18/AmberTools/src/mpich-3.2.1' Makefile:38608: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/home/jan/amber18/AmberTools/src/mpich-3.2.1' Makefile:10337: recipe for target 'all' failed make: *** [all] Error 2 below is the make file code close to line 39284. I have underlined the corresponding log file output and the make file line 39284 # normally built by autogen.sh, but this rebuild rule is here $(top_srcdir)/src/util/cvar/mpich_cvars.c: $(top_srcdir)/maint/extractcvars *( cd $(top_srcdir) && $(top_srcdir)/maint/extractcvars --dirs="`cat $(top_srcdir)/maint/cvardirs`")* $(cxx_buildiface_out_files): src/binding/cxx/buildiface-stamp src/binding/cxx/buildiface-stamp: $(top_srcdir)/src/binding/cxx/buildiface $(top_srcdir)/src/include/mpi.h.in ( cd $(top_srcdir)/src/binding/cxx && ./buildiface -nosep -initfile=cxx.vlist ) If you are able to provide any pointers it would be much appreciated.. Jan Szubert _______________________________________________ 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] Infiniband
by Kenneth Raffenetti 01 May '18

01 May '18

If MPICH was built in a default configuration, it will use sockets. To use MPICH with Infiniband, I'll need to know a little more about your system. I will contact you off list. Ken On 04/27/2018 06:39 PM, Mayank Jain wrote: > Hello, > > I am new to MPICH and I have cluster which MPICH installed. I wanted to check if MPICH is using Infiniband or sockets for transmission. Is their any way I can check same? > > Thanks, > Mayank > _______________________________________________ > 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] Using MPICH and Hydra to manage apruns
by Kenneth Raffenetti 01 May '18

01 May '18

Hi Justin, You can disable cobalt by adding this to your Hydra/MPICH configure: --with-hydra-bss=user,ssh,rsh,fork,slurm,ll,lsf,sge,pbs,manual,persist This is basically the default setting minus cobalt. Ken On 04/27/2018 10:37 AM, Justin M Wozniak wrote: > Hi > I am trying to use an MPI program to manage an ensemble of apruns > under Cobalt on Theta. I compiled an MPICH 3.2 for the login node. > Then, in an interactive allocation, I do: > > $ hostname > thetamom2 > > $ mpiexec -launcher fork -n 1 echo hi > [mpiexec@thetamom2] HYDU_parse_hostfile (utils/args/args.c:319): unable > to open host file: /var/tmp/cobalt.222331 > [mpiexec@thetamom2] HYDT_bscd_cobalt_query_node_list > (tools/bootstrap/external/cobalt_query_node_list.c:27): error parsing > hostfile > [mpiexec@thetamom2] HYDT_bsci_query_node_list > (tools/bootstrap/src/bsci_query_node_list.c:19): RMK returned error > while querying node list > [mpiexec@thetamom2] main (ui/mpich/mpiexec.c:186): unable to query the > RMK for a node list > > It looks like Hydra has detected that it is under Cobalt. How do I > force it to ignore Cobalt? > > Ultimately, I plan to replace 'echo' with a shell script that does an > aprun. > > Thanks > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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