April 2014 - discuss - mailman3.cels.anl.gov

Re: [mpich-discuss] c.txt and m.txt
by Mojtaba S. Moghani 07 Apr '14

07 Apr '14

On 2014-04-07 00:31, Reuti wrote: > Am 06.04.2014 um 21:32 schrieb Mojtaba S. Moghani: > >> According to the manual, the mpiexec command after building and installing doesnt work, what is the problem? > > To what do you refer by "doesnt work"? > > - command not found > - generates an error message when executed > - runs the given application, but only in serial > - runs in parallel but results in wrong results > ... > > -- Reuti > >> regards, <c.txt><m.txt>_______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss [1] > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss [1] After this commad : mpiexec -n 5 -f machinefile ./examples/cpi, it has some errors when run, errors like : HYDU_parse_hostfile (/home/mojtaba/libraries/mpich-3.1/src/pm/hydra/utils/args/args.c:319): unable to open host file: machinefile [mpiexec@Mojtaba] mfile_fn (/home/mojtaba/libraries/mpich-3.1/src/pm/hydra/ui/mpich/utils.c:336): error parsing hostfile [mpiexec@Mojtaba] match_arg (/home/mojtaba/libraries/mpich-3.1/src/pm/hydra/utils/args/args.c:152): match handler returned error [mpiexec@Mojtaba] HYDU_parse_array (/home/mojtaba/libraries/mpich-3.1/src/pm/hydra/utils/args/args.c:174): argument matching returned error [mpiexec@Mojtaba] parse_args (/home/mojtaba/libraries/mpich-3.1/src/pm/hydra/ui/mpich/utils.c:1596): error parsing input array [mpiexec@Mojtaba] HYD_uii_mpx_get_parameters (/home/mojtaba/libraries/mpich-3.1/src/pm/hydra/ui/mpich/utils.c:1648): unable to parse user arguments [mpiexec@Mojtaba] main (/home/mojtaba/libraries/mpich-3.1/src/pm/hydra/ui/mpich/mpiexec.c:153): error parsing parameters what is the problem? thanks, -- Mojtaba S. Moghani Faculty of Environment University of Tehran Links: ------ [1] https://lists.mpich.org/mailman/listinfo/discuss

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mpich2 - checkpointing error
by Marcelo Paiva Ramos 07 Apr '14

07 Apr '14

Hi, Can you help me to solve this problem? cat /etc/issue CentOS release 6.5 (Final) Kernel \r on an \m uname -a Linux server 2.6.32-431.11.2.el6.x86_64 #1 SMP Tue Mar 25 19:59:55 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux *INSTALL: blcr-0.8.5* tar xzvf blcr-0.8.5.tar.gz cd blcr-0.8.5 mkdir builddir cd builddir ../configure --prefix=/opt/blcr make make install /sbin/insmod /opt/blcr/lib/blcr/2.6.32-431.11.2.el6.x86_64/blcr_imports.ko /sbin/insmod /opt/blcr/lib/blcr/2.6.32-431.11.2.el6.x86_64/blcr.ko uname -r 2.6.32-431.11.2.el6.x86_64 lsmod | grep blcr blcr 115465 0 blcr_imports 10715 1 blcr ldconfig -p | grep blcr libcr_run.so.0 (libc6,x86-64) => /opt/blcr/lib/libcr_run.so.0 libcr_run.so (libc6,x86-64) => /opt/blcr/lib/libcr_run.so libcr_omit.so.0 (libc6,x86-64) => /opt/blcr/lib/libcr_omit.so.0 libcr_omit.so (libc6,x86-64) => /opt/blcr/lib/libcr_omit.so libcr.so.0 (libc6,x86-64) => /opt/blcr/lib/libcr.so.0 libcr.so (libc6,x86-64) => /opt/blcr/lib/libcr.so chkconfig --list | grep blcr blcr 0:off 1:off 2:on 3:on 4:on 5:on 6:off *INSTALL: mpich-3.1* tar xzvf mpich-3.1.tar.gz cd mpich-3.1 ./configure --disable-fast CFLAGS=-O2 FFLAGS=-O2 CXXFLAGS=-O2 FCFLAGS=-O2 --prefix=/opt/mpich2/ CC=/opt/intel/bin/icc FC=/opt/intel/bin/ifort F77=/opt/intel/bin/ifort --enable-checkpointing --with-hydra-ckpointlib=blcr --with-blcr=/opt/blcr --with-blcr-include=/opt/blcr/include --with-blcr-lib=/opt/blcr/lib make make install *.bashrc* export PATH=$PATH:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/blcr/bin:/opt/mpich2/bin export LD_LIBRARY_PATH=/usr/local/lib:/usr/local/lib64:/opt/intel/lib/intel64:/opt/blcr/lib:/opt/mpich2/lib *mpiexec -info* HYDRA build details: Version: 3.1 Release Date: Thu Feb 20 11:41:13 CST 2014 CC: /opt/intel/bin/icc -O2 CXX: g++ -O2 F77: /opt/intel/bin/ifort -O2 F90: /opt/intel/bin/ifort -O2 Configure options: '--disable-option-checking' '--prefix=/opt/mpich2' '--disable-fast' 'CFLAGS=-O2 -O0' 'FFLAGS=-O2 -O0' 'CXXFLAGS=-O2 ' 'FCFLAGS=-O2 ' 'CC=/opt/intel/bin/icc' 'FC=/opt/intel/bin/ifort' 'F77=/opt/intel/bin/ifort' '--enable-checkpointing' '--with-hydra-ckpointlib=blcr' '--with-blcr=/opt/blcr' '--with-blcr-include=/opt/blcr/include' '--with-blcr-lib=/opt/blcr/lib' '--cache-file=/dev/null' '--srcdir=.' 'LDFLAGS= -L/opt/blcr/lib' 'LIBS=-lrt -lcr -lpthread ' 'CPPFLAGS= -I/root/mpich-3.1/src/mpl/include -I/root/mpich-3.1/src/mpl/include -I/root/mpich-3.1/src/openpa/src -I/root/mpich-3.1/src/openpa/src -I/root/mpich-3.1/src/mpi/romio/include -I/opt/blcr/include' Process Manager: pmi Launchers available: ssh rsh fork slurm ll lsf sge pbs 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 *ERROR* mpiexec -n 1 -ckpointlib blcr -ckpoint-interval 20 -ckpoint-prefix /home/marcelo/TESTE/ ./teste [proxy:0:0@server] requesting checkpoint [proxy:0:0@server] checkpoint completed [proxy:0:0@server] HYDT_ckpoint_blcr_checkpoint (tools/ckpoint/blcr/ckpoint_blcr.c:241): Checkpointing failed. Make sure BLCR kernel module is loaded. Unknown error 2356 [proxy:0:0@server] ckpoint_thread (tools/ckpoint/ckpoint.c:76): blcr checkpoint returned error [proxy:0:0@server] requesting checkpoint [proxy:0:0@server] checkpoint completed [proxy:0:0@server] HYDT_ckpoint_blcr_checkpoint (tools/ckpoint/blcr/ckpoint_blcr.c:241): Checkpointing failed. Make sure BLCR kernel module is loaded. Unknown error 2356 [proxy:0:0@server] ckpoint_thread (tools/ckpoint/ckpoint.c:76): blcr checkpoint returned error Best regards, Marcelo.

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statically linked mpiexec
by Andy May 07 Apr '14

07 Apr '14

Hi, Does anyone know if there is a supported or recommended way to build MPICH such that it's binaries (eg. mpiexec) are statically linked? At present, post building I'm running: cd src/pm/hydra eval ./configure `./config.status --config` --disable-pci --disable-libxml2 make CCLD='$(CC) -all-static' which just disables two cases where the static libraries aren't available, then links statically, but is there a better or correct way to do this? Many thanks, Andy

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Re: [mpich-discuss] c.txt and m.txt
by Mojtaba S. Moghani 07 Apr '14

07 Apr '14

after this command : mpiexec -n 5 -f machinefile ./examples/cpi, it said that "error parsing hostfile" and "unable to parse user arguments" and "error parsing parameters" and something like these, so what is the problem? On 2014-04-07 00:31, Reuti wrote: > Am 06.04.2014 um 21:32 schrieb Mojtaba S. Moghani: > >> According to the manual, the mpiexec command after building and installing doesnt work, what is the problem? > > To what do you refer by "doesnt work"? > > - command not found > - generates an error message when executed > - runs the given application, but only in serial > - runs in parallel but results in wrong results > ... > > -- Reuti > >> regards, <c.txt><m.txt>_______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss [1] > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss [1] -- Mojtaba S. Moghani Faculty of Environment University of Tehran Links: ------ [1] https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] misc.h(28): catastrophic error: #error directive: "unknown size forunsigned int."
by Gilles Gouaillardet 06 Apr '14

06 Apr '14

Hi, i cannot reproduce this in my environment, this should be something specific to yours can you please run grep HWLOC_SIZEOF_UNSIGNED_INT src/pm/hydra/tools/topo/hwloc/hwloc/include/private/autogen/config.h this should return #define HWLOC_SIZEOF_UNSIGNED_INT 4 then in src/pm/hydra/tools/topo/hwloc/hwloc/include/private/misc.h, at line 23, add the following four lines #define STRINGIFY(s) XSTRINGIFY(s) #define XSTRINGIFY(s) #s #pragma message ("HWLOC_SIZEOF_UNSIGNED_INT " STRINGIFY(HWLOC_SIZEOF_UNSIGNED_INT)) #pragma message ("HWLOC_BITS_PER_INT " STRINGIFY(HWLOC_BITS_PER_INT)) and then recompile : cd src/pm/hydra/tools/topo/hwloc/hwloc/src make traversal.o this should return /.../src/pm/hydra/tools/topo/hwloc/hwloc/include/private/misc.h:25: note: #pragma message: HWLOC_SIZEOF_UNSIGNED_INT 4 /.../src/pm/hydra/tools/topo/hwloc/hwloc/include/private/misc.h:26: note: #pragma message: HWLOC_BITS_PER_INT (4 * 8) Cheers, Gilles On 2014/04/06 21:53, 童伟 wrote: > I tried with gcc, got errors during make, too. > > [weitong@magnetics tmp_GNU]$ ../configure --prefix=/usr/local/mpich3_GNU CC=gcc CXX=g++ FC=gfortran --enable-threads=multiple --with-pm=mpd:hydra 2>&1 | tee c.txt > [weitong@magnetics tmp_GNU]$ make 2>&1 | tee m.txt > > make[4]: Entering directory `/home/weitong/setup/mpich/mpich-3.1/tmp_GNU/src/pm/hydra/tools/topo/hwloc/hwloc/src' > CC topology.lo > CC traversal.lo > In file included from ../../../../../../../../../src/pm/hydra/tools/topo/hwloc/hwloc/src/traversal.c:12: > /home/weitong/setup/mpich/mpich-3.1/src/pm/hydra/tools/topo/hwloc/hwloc/include/private/misc.h:28:2: error: #error "unknown size for unsigned int." >

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Re: [mpich-discuss] c.txt and m.txt
by Reuti 06 Apr '14

06 Apr '14

Am 06.04.2014 um 21:32 schrieb Mojtaba S. Moghani: > According to the manual, the mpiexec command after building and installing doesnt work, what is the problem? To what do you refer by "doesnt work"? - command not found - generates an error message when executed - runs the given application, but only in serial - runs in parallel but results in wrong results ... -- Reuti > regards, > > > <c.txt><m.txt>_______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

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c.txt and m.txt
by Mojtaba S. Moghani 06 Apr '14

06 Apr '14

According to the manual, the mpiexec command after building and installing doesnt work, what is the problem? regards,

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file open error code checking
by Wei-keng Liao 06 Apr '14

06 Apr '14

I can see error codes EISDIR and EEXIST are checked in ad_ufs_open.c and the corresponding MPI_ERR_BAD_FILE and MPI_ERR_FILE_EXISTS are generated. But this update does not appear on other file systems, such as Lustre and GPFS. PnetCDF needs an MPI-IO that can return the MPI_ERR_FILE_EXISTS class when the MPI_MODE_EXCL mode is set and the file exist. This class will correspond to NC_EEXIST in PnetCDF (when NC_NOCLOBBER is set in ncmpi_create and file exists). ad_ufs_open.c 94 else if(errno == EISDIR) { 95 *error_code = MPIO_Err_create_code(MPI_SUCCESS, 96 MPIR_ERR_RECOVERABLE, myname, 97 __LINE__, MPI_ERR_BAD_FILE, 98 "**filename", 0); 99 } 100 else if(errno == EEXIST) { 101 *error_code = MPIO_Err_create_code(MPI_SUCCESS, 102 MPIR_ERR_RECOVERABLE, myname, 103 __LINE__, MPI_ERR_FILE_EXISTS, 104 "**fileexist", 0); 105 106 } Wei-keng

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Re: [mpich-discuss] misc.h(28): catastrophic error: #error directive: "unknown size forunsigned int."
by 童伟 06 Apr '14

06 Apr '14

I tried with gcc, got errors during make, too. [weitong@magnetics tmp_GNU]$ ../configure --prefix=/usr/local/mpich3_GNU CC=gcc CXX=g++ FC=gfortran --enable-threads=multiple --with-pm=mpd:hydra 2>&1 | tee c.txt [weitong@magnetics tmp_GNU]$ make 2>&1 | tee m.txt make[4]: Entering directory `/home/weitong/setup/mpich/mpich-3.1/tmp_GNU/src/pm/hydra/tools/topo/hwloc/hwloc/src' CC topology.lo CC traversal.lo In file included from ../../../../../../../../../src/pm/hydra/tools/topo/hwloc/hwloc/src/traversal.c:12: /home/weitong/setup/mpich/mpich-3.1/src/pm/hydra/tools/topo/hwloc/hwloc/include/private/misc.h:28:2: error: #error "unknown size for unsigned int." make[4]: *** [traversal.lo] error 1 make[4]: Leaving directory `/home/weitong/setup/mpich/mpich-3.1/tmp_GNU/src/pm/hydra/tools/topo/hwloc/hwloc/src' make[3]: *** [all-recursive] error 1 make[3]: Leaving directory `/home/weitong/setup/mpich/mpich-3.1/tmp_GNU/src/pm/hydra/tools/topo/hwloc/hwloc' make[2]: *** [all-recursive] error 1 make[2]: Leaving directory `/home/weitong/setup/mpich/mpich-3.1/tmp_GNU/src/pm/hydra' make[1]: *** [all-recursive] error 1 make[1]: Leaving directory `/home/weitong/setup/mpich/mpich-3.1/tmp_GNU' make: *** [all] error 2 -----原始邮件----- 发件人: "Wesley Bland" <wbland(a)anl.gov> 发送时间: 2014年4月4日星期五收件人: "discuss(a)mpich.org" <discuss(a)mpich.org> 抄送: 主题: Re: [mpich-discuss] misc.h(28): catastrophic error: #error directive: "unknown size forunsigned int." Can you send us your config.log? On Fri, Apr 4, 2014 at 4:24 AM, Wei TOng <weitong(a)hmfl.ac.cn> wrote: Dear everyone, I am installing mpich3.1 with Intel parallel_studio_xe_2011_sp1_update3 (ifort12). My configure is #./configure --prefix=/usr/local/mpich_intel CC=icc CXX=icpc F77=ifort FC=ifort --enable-threads=multiple --with-pm=mpd:hydra 2>&1 | tee c.txt Which completed successfully. But when I make, finally I got following errors: /home/weitong/setup/mpich-3.1/src/pm/hydra/tools/topo/hwloc/hwloc/include/private/misc.h(28): catastrophic error: #error directive: "unknown size for unsigned int." #error "unknown size for unsigned int." ^ compilation aborted for traversal.c (code 4) make[4]: *** [traversal.lo] error 1 make[4]: Leaving directory `/home/weitong/setup/mpich-3.1/src/pm/hydra/tools/topo/hwloc/hwloc/src' make[3]: *** [all-recursive] error 1 make[3]: Leaving directory `/home/weitong/setup/mpich-3.1/src/pm/hydra/tools/topo/hwloc/hwloc' make[2]: *** [all-recursive] error 1 make[2]: Leaving directory `/home/weitong/setup/mpich-3.1/src/pm/hydra' make[1]: *** [all-recursive] error 1 make[1]: Leaving directory `/home/weitong/setup/mpich-3.1' make: *** [all] 错误 2 PS: I also tried "mpich-master-v3.1-137-gb912961f", the same errors during make. Any solutions? Best, Wei Tong _______________________________________________ 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 class MPI_ERR_NO_SUCH_FILE thrown by MPI_File_delete
by Wei-keng Liao 05 Apr '14

05 Apr '14

Sorry, the code should check errno instead of err. 19 err = unlink(filename); if (err == -1) { int err_class = MPI_ERR_IO; if (errno == ENOENT) err_class = MPI_ERR_NO_SUCH_FILE; *error_code = MPIO_Err_create_code(MPI_SUCCESS, MPIR_ERR_RECOVERABLE, myname, __LINE__, err_class, "**io", "**io %s", strerror(errno)); return; } Wei-keng On Apr 5, 2014, at 2:48 PM, Wei-keng Liao wrote: > In MPI-2 standard has the sentence below for MPI_File_delete. > "If the file does not exist, MPI_FILE_DELETE raises an error in the class MPI_ERR_NO_SUCH_FILE." > > But in src/mpi/romio/adio/common/ad_delete.c, the return code of unlink() is not checked > for this error (only MPI_ERR_IO class is thrown.) May I suggest to add a check, so the > MPI_ERR_NO_SUCH_FILE class can reported. > > 19 err = unlink(filename); > if (err == ENOENT) { > *error_code = MPIO_Err_create_code(MPI_SUCCESS, MPIR_ERR_RECOVERABLE, > myname, __LINE__, MPI_ERR_NO_SUCH_FILE, "**io", > "**io %s", strerror(errno)); > return; > } > else if (err == -1) { > ... > > Wei-keng > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

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