June 2016 - discuss - mailman3.cels.anl.gov

installation
by phani sri 09 Jun '16

09 Jun '16

I am a new user of FLASH4.3, which initiating the sample programme Sedov in 2d, I am not able to build it because when execute make it is showing the following error, I have installed the mpich2 in /usr/local but the following error it is showing. Can any one give a suggestion. Thank You -- D. P. S. L. Kameswari, Ph. D(Physics) ACRHEM University Of Hyderabad, Hyderabad, e-mail:[email protected] <id%3Aphanisri123(a)gmail.com> _______________________________________________ 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] stdin redirection
by Thakur, Rajeev 08 Jun '16

08 Jun '16

You could read the input parameters by storing them in a text file and then using fopen and fscanf. Rajeev > On Jun 8, 2016, at 7:50 AM, Filippone, Salvatore <Salvatore.Filippone(a)cranfield.ac.uk> wrote: > > The key term here is "larg(ish)", which I used in my original email to > mean something larger than the limit I was hitting (64KB) but not > *really* large (in my original case I was using a file of around 300KB). > I naturally moved to normal file I/O; MPI I/O was not quite called for, > because these were just the control parameters for a series of benchmark > runs, not actual input data (which was read and handled separately). > > Thanks > Salvatore > > On Wed, 2016-06-08 at 12:46 +0000, Balaji, Pavan wrote: >> If you want to read large files, you should really use MPI-I/O, not >> stdin. We support reading from stdin for users who migrate from >> sequential programs to parallel programming, but that's not meant to be >> the real mechanism to read files. I'm not supportive of trying to >> modify mpich for such use cases. >> >> -- Pavan >> >>> On Jun 5, 2016, at 11:18 AM, Seo, Sangmin <sseo at anl.gov> wrote: >>> >>> Hello Salvatore, >>> >>> The current MPICH uses pipe to redirect stdin to processes, but pipe >> has a limited capacity (e.g., 64KB in Linux. Please refer to >> http://man7.org/linux/man-pages/man7/pipe.7.html) Therefore, if we >> redirect a file, which is larger than the pipe capacity, to stdin, the >> current MPICH implementation is not handling it properly because write() >> does not succeed to write a large data (> the pipe capacity) to the pipe >> for stdin. >>> >>> I created a ticket for this issue >> (https://trac.mpich.org/projects/mpich/ticket/2336) but I'd recommend >> you to use file I/O in order to handle a large file instead of using >> stdin redirection. >>> >>> — Sangmin >>> >>> > > _______________________________________________ > 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] stdin redirection
by Filippone, Salvatore 08 Jun '16

08 Jun '16

The key term here is "larg(ish)", which I used in my original email to mean something larger than the limit I was hitting (64KB) but not *really* large (in my original case I was using a file of around 300KB). I naturally moved to normal file I/O; MPI I/O was not quite called for, because these were just the control parameters for a series of benchmark runs, not actual input data (which was read and handled separately). Thanks Salvatore On Wed, 2016-06-08 at 12:46 +0000, Balaji, Pavan wrote: > If you want to read large files, you should really use MPI-I/O, not > stdin. We support reading from stdin for users who migrate from > sequential programs to parallel programming, but that's not meant to be > the real mechanism to read files. I'm not supportive of trying to > modify mpich for such use cases. > > -- Pavan > > > On Jun 5, 2016, at 11:18 AM, Seo, Sangmin <sseo at anl.gov> wrote: > > > > Hello Salvatore, > > > > The current MPICH uses pipe to redirect stdin to processes, but pipe > has a limited capacity (e.g., 64KB in Linux. Please refer to > http://man7.org/linux/man-pages/man7/pipe.7.html) Therefore, if we > redirect a file, which is larger than the pipe capacity, to stdin, the > current MPICH implementation is not handling it properly because write() > does not succeed to write a large data (> the pipe capacity) to the pipe > for stdin. > > > > I created a ticket for this issue > (https://trac.mpich.org/projects/mpich/ticket/2336) but I'd recommend > you to use file I/O in order to handle a large file instead of using > stdin redirection. > > > > — Sangmin > > > > _______________________________________________ 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-master-v3.2-331-g44fd9c5f39e5: problem with MPMD programs
by Siegmar Gross 08 Jun '16

08 Jun '16

Hi, I have built mpich-master-v3.2-331-g44fd9c5f39e5 on my machines (Solaris 10 Sparc, Solaris 10 x86_64, and openSUSE Linux 12.1 x86_64) with gcc-5.1.0 and Sun C 5.13. Unfortunately I get an error if I try to specify different host lists for the master and slave program. linpc1 hello_2 116 mpiexec -np 1 --host sunpc1 hello_2_mpi : -np 2 --host sunpc1,linpc1 hello_2_slave_mpi [mpiexec@linpc1] hostlist_fn (../../../../mpich-master-v3.2-331-g44fd9c5f39e5/src/pm/hydra/ui/mpich/utils.c:373): duplicate host file or host list setting [mpiexec@linpc1] match_arg (../../../../mpich-master-v3.2-331-g44fd9c5f39e5/src/pm/hydra/utils/args/args.c:152): match handler returned error [mpiexec@linpc1] HYDU_parse_array (../../../../mpich-master-v3.2-331-g44fd9c5f39e5/src/pm/hydra/utils/args/args.c:174): argument matching returned error [mpiexec@linpc1] parse_args (../../../../mpich-master-v3.2-331-g44fd9c5f39e5/src/pm/hydra/ui/mpich/utils.c:1597): error parsing input array [mpiexec@linpc1] HYD_uii_mpx_get_parameters (../../../../mpich-master-v3.2-331-g44fd9c5f39e5/src/pm/hydra/ui/mpich/utils.c:1649): unable to parse user arguments [mpiexec@linpc1] main (../../../../mpich-master-v3.2-331-g44fd9c5f39e5/src/pm/hydra/ui/mpich/mpiexec.c:149): error parsing parameters linpc1 hello_2 117 I would be grateful if somebody can fix the problem. Please let me know, if you need more information. 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-master-v3.2-331-g44fd9c5f39e5: runtime error spawning processes
by Siegmar Gross 08 Jun '16

08 Jun '16

Hi, I have built mpich-master-v3.2-331-g44fd9c5f39e5 on my machines (Solaris 10 Sparc, Solaris 10 x86_64, and openSUSE Linux 12.1 x86_64) with gcc-5.1.0 and Sun C 5.13. Most of the time I get an error with different error messages spawning processes on a Sparc machine. tyr spawn 107 mpiexec -np 1 --host tyr,tyr,tyr,tyr,tyr spawn_master Parent process 0 running on tyr.informatik.hs-fulda.de I create 4 slave processes Parent process 0: tasks in MPI_COMM_WORLD: 1 tasks in COMM_CHILD_PROCESSES local group: 1 tasks in COMM_CHILD_PROCESSES remote group: 4 Slave process 0 of 4 running on tyr.informatik.hs-fulda.de Slave process 1 of 4 running on tyr.informatik.hs-fulda.de Slave process 2 of 4 running on tyr.informatik.hs-fulda.de Slave process 3 of 4 running on tyr.informatik.hs-fulda.de spawn_slave 0: argv[0]: spawn_slave spawn_slave 1: argv[0]: spawn_slave spawn_slave 2: argv[0]: spawn_slave spawn_slave 3: argv[0]: spawn_slave tyr spawn 108 mpiexec -np 1 --host tyr,tyr,tyr,tyr,tyr spawn_master Parent process 0 running on tyr.informatik.hs-fulda.de I create 4 slave processes Fatal error in MPI_Comm_spawn: Unknown error class, error stack: MPI_Comm_spawn(141)...................: MPI_Comm_spawn(cmd="spawn_slave", argv=0, maxprocs=4, MPI_INFO_NULL, root=0, MPI_COMM_WORLD, intercomm=ffffffff7fffdf58, errors=0) failed MPIDI_Comm_spawn_multiple(274)........: MPID_Comm_accept(153).................: MPIDI_Comm_accept(1039)...............: MPIDU_Complete_posted_with_error(1137): Process failed tyr spawn 109 tyr spawn 111 mpiexec -np 1 --host tyr,tyr,tyr,tyr,tyr spawn_master Parent process 0 running on tyr.informatik.hs-fulda.de I create 4 slave processes =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = PID 3322 RUNNING AT tyr = EXIT CODE: 10 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES =================================================================================== [proxy:0:[email protected]] HYD_pmcd_pmip_control_cmd_cb (../../../../mpich-master-v3.2-331-g44fd9c5f39e5/src/pm/hydra/pm/pmiserv/pmip_cb.c:883): assert (!closed) failed [proxy:0:[email protected]] HYDT_dmxu_poll_wait_for_event (../../../../mpich-master-v3.2-331-g44fd9c5f39e5/src/pm/hydra/tools/demux/demux_poll.c:77): callback returned error status [proxy:0:[email protected]] main (../../../../mpich-master-v3.2-331-g44fd9c5f39e5/src/pm/hydra/pm/pmiserv/pmip.c:202): demux engine error waiting for event [mpiexec(a)tyr.informatik.hs-fulda.de] HYDT_bscu_wait_for_completion (../../../../mpich-master-v3.2-331-g44fd9c5f39e5/src/pm/hydra/tools/bootstrap/utils/bscu_wait.c:76): one of the processes terminated badly; aborting [mpiexec(a)tyr.informatik.hs-fulda.de] HYDT_bsci_wait_for_completion (../../../../mpich-master-v3.2-331-g44fd9c5f39e5/src/pm/hydra/tools/bootstrap/src/bsci_wait.c:23): launcher returned error waiting for completion [mpiexec(a)tyr.informatik.hs-fulda.de] HYD_pmci_wait_for_completion (../../../../mpich-master-v3.2-331-g44fd9c5f39e5/src/pm/hydra/pm/pmiserv/pmiserv_pmci.c:218): launcher returned error waiting for completion [mpiexec(a)tyr.informatik.hs-fulda.de] main (../../../../mpich-master-v3.2-331-g44fd9c5f39e5/src/pm/hydra/ui/mpich/mpiexec.c:340): process manager error waiting for completion tyr spawn 112 I would be grateful if somebody can fix the problem. Please let me know, if you need more information. 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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Re: [mpich-discuss] Problem in installation
by Kenneth Raffenetti 06 Jun '16

06 Jun '16

On 06/06/2016 02:22 AM, phani sri wrote: > I am having a problem in installing MPICH in my Ubuntu OS. I would > like to know about the following issues: > 1) Are MPICH and MPICH2 are same or different. MPICH2 was renamed to just MPICH when version 3.0 was released. MPICH is the name of the software from now on. > 2) How can I check if MPICH is installed or not. Assuming the installation directory is in your PATH, you can run "mpichversion" to see if it is installed and what version. If you just installed using "apt-get install mpich" you should be mostly set. If you built from source and encountered and error, post it here and we can determine the issue. Ken _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Problem in installation
by phani sri 06 Jun '16

06 Jun '16

I am having a problem in installing MPICH in my Ubuntu OS. I would like to know about the following issues: 1) Are MPICH and MPICH2 are same or different. 2) How can I check if MPICH is installed or not. Thank You -- D. P. S. L. Kameswari, Ph. D(Physics) ACRHEM University Of Hyderabad, Hyderabad, e-mail:[email protected] <id%3Aphanisri123(a)gmail.com> _______________________________________________ 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] stdin redirection
by Balaji, Pavan 05 Jun '16

05 Jun '16

If you want to read large files, you should really use MPI-I/O, not stdin. We support reading from stdin for users who migrate from sequential programs to parallel programming, but that's not meant to be the real mechanism to read files. I'm not supportive of trying to modify mpich for such use cases. -- Pavan > On Jun 5, 2016, at 11:18 AM, Seo, Sangmin <sseo(a)anl.gov> wrote: > > Hello Salvatore, > > The current MPICH uses pipe to redirect stdin to processes, but pipe has a limited capacity (e.g., 64KB in Linux. Please refer to http://man7.org/linux/man-pages/man7/pipe.7.html). Therefore, if we redirect a file, which is larger than the pipe capacity, to stdin, the current MPICH implementation is not handling it properly because write() does not succeed to write a large data (> the pipe capacity) to the pipe for stdin. > > I created a ticket for this issue (https://trac.mpich.org/projects/mpich/ticket/2336) but I'd recommend you to use file I/O in order to handle a large file instead of using stdin redirection. > > — Sangmin > > >> On Jun 1, 2016, at 4:37 AM, Filippone, Salvatore <Salvatore.Filippone(a)cranfield.ac.uk> wrote: >> >> Hello, >> I have found something I do not understand with mpich 3.2.0. The >> problem started with an application, but to demonstrate it I have >> written a very simple-minded program which I am including here. >> The program simply reads lines from standard input and reprints them >> on standard output from a second process. >> >> Now if I redirect stdin from a small(ish) file it works as expected: >> ====================================================================== >> [sfilippo@localhost MPI_cat]$ mpicc -v >> mpicc for MPICH version 3.2 >> Using built-in specs. >> COLLECT_GCC=gcc >> COLLECT_LTO_WRAPPER=/opt/gnu/5.3.0/libexec/gcc/x86_64-unknown-linux- >> gnu/5.3.0/lto-wrapper >> Target: x86_64-unknown-linux-gnu >> Configured with: ../gcc-5.3.0/configure --prefix=/opt/gnu/5.3.0 -- >> enable-languages=c,c++,fortran --with- >> gmp=/usr/local/travel/GCC/BUILDS/gmp --with- >> mpfr=/usr/local/travel/GCC/BUILDS/mpfr --with- >> mpc=/usr/local/travel/GCC/BUILDS/mpc --with- >> isl=/usr/local/travel/GCC/BUILDS/isl >> Thread model: posix >> gcc version 5.3.0 (GCC) >> [sfilippo@localhost MPI_cat]$ mpicc -o mpicat mpicat.c >> [sfilippo@localhost MPI_cat]$ head mpicat.c | mpirun -np 2 ./mpicat >> #include <stdlib.h> >> #include <stdio.h> >> #include "mpi.h" >> #define LNSZ 129 >> #define TAGI 234 >> #define TAGC 567 >> int main(int argc, char *argv[] ) >> { >> char linebuf[LNSZ]; >> int ierr, iam, np, itmp ; >> [sfilippo@localhost MPI_cat]$ >> ====================================================================== >> However if I use a long(ish) file (such as a configure script) I get >> either no output or an error. On another machine with GNU 4.9.3 I >> always get the silent failure. >> ====================================================================== >> [sfilippo@localhost MPI_cat]$ mpirun -np 2 ./mpicat < configure >> [sfilippo@localhost MPI_cat]$ mpirun -np 2 ./mpicat < configure >> [proxy:0:[email protected]] HYD_pmcd_pmip_control_cmd_cb >> (../../../../mpich-3.2/src/pm/hydra/pm/pmiserv/pmip_cb.c:937): process >> reading stdin too slowly; can't keep up >> [proxy:0:[email protected]] HYDT_dmxu_poll_wait_for_event >> (../../../../mpich-3.2/src/pm/hydra/tools/demux/demux_poll.c:76): >> callback returned error status >> [proxy:0:[email protected]] main (../../../../mpich- >> 3.2/src/pm/hydra/pm/pmiserv/pmip.c:206): demux engine error waiting for >> event >> [sfilippo@localhost MPI_cat]$ >> ======================================================================= >> >> Am I missing something? >> Is this supposed to work? I could find nothing relevant in the FAQ >> >> Thanks a lot >> Salvatore >> -- >> Salvatore Filippone, PhD >> Centre for Computational Engineering Sciences, >> School of Aerospace, Transport and Manufacturing, Bldg 52 >> Cranfield University >> Cranfield >> MK43 0AL >> United Kingdom >> tel: +44(0) 1234 758361 >> >> <mpicat.c>_______________________________________________ >> 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

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Re: [mpich-discuss] Any past mpich version work with RHEL/CentOS7 verbs?
by Kenneth Raffenetti 05 Jun '16

05 Jun '16

Current MPICH (3.2) supports MXM with the configure options --with-device=ch3:nemesis:mxm and --with-mxm=<path-to-installation>. Ken On 06/05/2016 11:25 AM, Galloway, Michael D. wrote: > All, > > > Our cluster has centos7.2 libibverbs installed, we'd like to build an > mpich that will work with it if possible, I understand current versions > of mpich/mvapich have a requirement of OFED+MXM. We plan to deploy OFED > and MXM later this summer but we are wondering if there is any way to > get mpich working now with our environment. > > > --- michael > > > > > _______________________________________________ > 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] Any past mpich version work with RHEL/CentOS7 verbs?
by Galloway, Michael D. 05 Jun '16

05 Jun '16

?Great! I'll make a build and test, thanks! --- michael ________________________________ From: Jonathan Perkins <perkinjo(a)cse.ohio-state.edu> Sent: Sunday, June 05, 2016 12:48 PM To: discuss(a)mpich.org Subject: Re: [mpich-discuss] Any past mpich version work with RHEL/CentOS7 verbs? Hello. MXM is not required if you're using MVAPICH2. MVAPICH2 will work well with the ibverbs distributed by RHEL/CENTOS. On Sun, Jun 5, 2016, 12:27 PM Galloway, Michael D. <gallowaymd(a)ornl.gov<mailto:[email protected]>> wrote: ?All, Our cluster has centos7.2 libibverbs installed, we'd like to build an mpich that will work with it if possible, I understand current versions of mpich/mvapich have a requirement of OFED+MXM. We plan to deploy OFED and MXM later this summer but we are wondering if there is any way to get mpich working now with our environment. --- michael _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> 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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