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Re: [mpich-discuss] Compiler optimization flags in MPICH 3.0 rc1
by Darius Buntinas 16 Nov '12

16 Nov '12

There are certain warnings that the compiler will only check with optimization enabled. To get all warnings, -O2 must be included. -d On Nov 16, 2012, at 11:52 AM, Yauheni Zelenko wrote: > Hi, Darius! > > But why warnings flags are mixed with optimization ones? I think these options should be independent. > > Eugene. > ________________________________________ > From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] On Behalf Of Darius Buntinas [buntinas(a)mcs.anl.gov] > Sent: Friday, November 16, 2012 9:41 AM > To: discuss(a)mpich.org > Cc: mpich-discuss(a)mcs.anl.gov > Subject: Re: [mpich-discuss] Compiler optimization flags in MPICH 3.0 rc1 > > The --enable-strict flag adds -O2. Try --enable-strict=noopt. > > -d > > > On Nov 15, 2012, at 7:06 PM, Yauheni Zelenko wrote: > >> Hi! >> >> I tried to build optimize and debug version of MPICH 3.0 rc1 and noticed some problems with compiler optimization flags. Looks like -O2 is set implicitly. >> >> For optimize configuration command like contains -O2 and -O3: >> >> ./configure --prefix=${InstallDir} \ >> --with-pm=hydra --with-device=ch3:nemesis \ >> --disable-chekpointing \ >> --enable-strict --enable-fast=O3 \ >> --disable-f77 --disable-fc \ >> CC=${GCCDir}/bin/gcc CFLAGS="-m32 -fPIC" \ >> CPP=${GCCDir}/bin/cpp \ >> CXX=${GCCDir}/bin/g++ CXXFLAGS="-m32 -fPIC" \ >> CXXCPP=${GCCDir}/bin/cpp >> >> For debug one -O2, but optimization is disabled: >> >> ./configure --prefix=${InstallDir} \ >> --with-pm=hydra --with-device=ch3:nemesis \ >> --disable-chekpointing \ >> --enable-strict --disable-fast -enable-g=debug \ >> --disable-f77 --disable-fc \ >> CC=${GCCDir}/bin/gcc CFLAGS="-m32 -fPIC" \ >> CPP=${GCCDir}/bin/cpp \ >> CXX=${GCCDir}/bin/g++ CXXFLAGS="-m32 -fPIC" \ >> CXXCPP=${GCCDir}/bin/cpp >> >> Eugene. >> _______________________________________________ >> 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] Compiler optimization flags in MPICH 3.0 rc1
by Pavan Balaji 16 Nov '12

16 Nov '12

On 11/16/2012 11:52 AM US Central Time, Yauheni Zelenko wrote: > But why warnings flags are mixed with optimization ones? I think > these options should be independent. They are, unfortunately, not independent. Some compilers throw some errors only when the optimization flag is specified. That's the reason why we have both options --enable-strict and --enable-strict=noopt. -- Pavan -- Pavan Balaji http://www.mcs.anl.gov/~balaji

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Re: [mpich-discuss] Compiler optimization flags in MPICH 3.0 rc1
by Yauheni Zelenko 16 Nov '12

16 Nov '12

Hi, Darius! But why warnings flags are mixed with optimization ones? I think these options should be independent. Eugene. ________________________________________ From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] On Behalf Of Darius Buntinas [buntinas(a)mcs.anl.gov] Sent: Friday, November 16, 2012 9:41 AM To: discuss(a)mpich.org Cc: mpich-discuss(a)mcs.anl.gov Subject: Re: [mpich-discuss] Compiler optimization flags in MPICH 3.0 rc1 The --enable-strict flag adds -O2. Try --enable-strict=noopt. -d On Nov 15, 2012, at 7:06 PM, Yauheni Zelenko wrote: > Hi! > > I tried to build optimize and debug version of MPICH 3.0 rc1 and noticed some problems with compiler optimization flags. Looks like -O2 is set implicitly. > > For optimize configuration command like contains -O2 and -O3: > > ./configure --prefix=${InstallDir} \ > --with-pm=hydra --with-device=ch3:nemesis \ > --disable-chekpointing \ > --enable-strict --enable-fast=O3 \ > --disable-f77 --disable-fc \ > CC=${GCCDir}/bin/gcc CFLAGS="-m32 -fPIC" \ > CPP=${GCCDir}/bin/cpp \ > CXX=${GCCDir}/bin/g++ CXXFLAGS="-m32 -fPIC" \ > CXXCPP=${GCCDir}/bin/cpp > > For debug one -O2, but optimization is disabled: > > ./configure --prefix=${InstallDir} \ > --with-pm=hydra --with-device=ch3:nemesis \ > --disable-chekpointing \ > --enable-strict --disable-fast -enable-g=debug \ > --disable-f77 --disable-fc \ > CC=${GCCDir}/bin/gcc CFLAGS="-m32 -fPIC" \ > CPP=${GCCDir}/bin/cpp \ > CXX=${GCCDir}/bin/g++ CXXFLAGS="-m32 -fPIC" \ > CXXCPP=${GCCDir}/bin/cpp > > Eugene. > _______________________________________________ > 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] MPI i/o like fopen (filename, "rb")
by Jeff Hammond 16 Nov '12

16 Nov '12

You can Google or go to http://www.mcs.anl.gov/research/projects/mpi/www/www3/ to get documentation for how to use the following commands: MPI_File_get_size MPI_File_open MPI_File_read MPI_File_write MPI_File_close These are the ones you need to do a straightforward conversion of your code. Best, Jeff On Fri, Nov 16, 2012 at 11:34 AM, Muhammad Zulfikar Handana <zulfikarhandana(a)gmail.com> wrote: > dear, > i have a little confused about MPI i/o, because iam new for this > programming. i have some question. > if i want make some program with this code > > 1) > > int get_size(char *filename) > { > struct stat buf; > stat(filename,&buf); > int j =buf.st_size; > > return j; > } > > 2) > key = fopen(key_file, "rb"); > fread(Kunci, pk, 1, key); > for(i=0;i<Nk*4;i++) > Key[i]=Kunci[i]; > > 3) hasil = fopen (file_akhir, "wb"); > for (k=0;k<(((block-1)*16)+pad);k++) > { > fputc(output[k], hasil); > } > fclose (hasil); > > how to translate that code into MPI i / o ? > thanks a lot for your attention > > Regards > > > Handana > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- Jeff Hammond Argonne Leadership Computing Facility University of Chicago Computation Institute jhammond(a)alcf.anl.gov / (630) 252-5381 http://www.linkedin.com/in/jeffhammond https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond

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Re: [mpich-discuss] Compiler optimization flags in MPICH 3.0 rc1
by Darius Buntinas 16 Nov '12

16 Nov '12

The --enable-strict flag adds -O2. Try --enable-strict=noopt. -d On Nov 15, 2012, at 7:06 PM, Yauheni Zelenko wrote: > Hi! > > I tried to build optimize and debug version of MPICH 3.0 rc1 and noticed some problems with compiler optimization flags. Looks like -O2 is set implicitly. > > For optimize configuration command like contains -O2 and -O3: > > ./configure --prefix=${InstallDir} \ > --with-pm=hydra --with-device=ch3:nemesis \ > --disable-chekpointing \ > --enable-strict --enable-fast=O3 \ > --disable-f77 --disable-fc \ > CC=${GCCDir}/bin/gcc CFLAGS="-m32 -fPIC" \ > CPP=${GCCDir}/bin/cpp \ > CXX=${GCCDir}/bin/g++ CXXFLAGS="-m32 -fPIC" \ > CXXCPP=${GCCDir}/bin/cpp > > For debug one -O2, but optimization is disabled: > > ./configure --prefix=${InstallDir} \ > --with-pm=hydra --with-device=ch3:nemesis \ > --disable-chekpointing \ > --enable-strict --disable-fast -enable-g=debug \ > --disable-f77 --disable-fc \ > CC=${GCCDir}/bin/gcc CFLAGS="-m32 -fPIC" \ > CPP=${GCCDir}/bin/cpp \ > CXX=${GCCDir}/bin/g++ CXXFLAGS="-m32 -fPIC" \ > CXXCPP=${GCCDir}/bin/cpp > > Eugene. > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

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MPI i/o like fopen (filename, "rb")
by Muhammad Zulfikar Handana 16 Nov '12

16 Nov '12

dear, i have a little confused about MPI i/o, because iam new for this programming. i have some question. if i want make some program with this code 1) int get_size(char *filename) { struct stat buf; stat(filename,&buf); int j =buf.st_size; return j; } 2) key = fopen(key_file, "rb"); fread(Kunci, pk, 1, key); for(i=0;i<Nk*4;i++) Key[i]=Kunci[i]; 3) hasil = fopen (file_akhir, "wb"); for (k=0;k<(((block-1)*16)+pad);k++) { fputc(output[k], hasil); } fclose (hasil); how to translate that code into MPI i / o ? thanks a lot for your attention Regards Handana

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Re: [mpich-discuss] crash mpiexec
by NARDI Luigi 16 Nov '12

16 Nov '12

Hello, Thanks for your response. For the master node on Windows I copy past the core dump analysis. It seems there is something wrong with the function: PMPI_Wtime. I had some problems on generating the core dump file on the ARM side. I can on a normal linux x86 system but not on the CARMA. This concerns the 4 slave nodes. Anyway, I guess that the crash comes from the master node. As I said in my previous email the example I run is a trivial test case. May be this crash comes from something wrong on mpiexec working on heterogeneous clusters (Windows/Linux and x86/ARM)? Thanks Luigi Core: Windows XP Version 2600 (Service Pack 3) MP (4 procs) Free x86 compatible Product: WinNt, suite: SingleUserTS Machine Name: Debug session time: Fri Nov 9 12:08:23.000 2012 (UTC - 5:00) System Uptime: 0 days 0:05:01.858 Process Uptime: 0 days 0:00:01.000 Kernel time: 0 days 0:00:00.000 User time: 0 days 0:00:00.000 TRIAGER: Could not open triage file : e:\dump_analysis\program\triage\oca.ini, error 2 TRIAGER: Could not open triage file : e:\dump_analysis\program\winxp\triage.ini, error 2 TRIAGER: Could not open triage file : e:\dump_analysis\program\triage\user.ini, error 2 *** ERROR: Symbol file could not be found. Defaulted to export symbols for mpich2.dll - *** ERROR: Module load completed but symbols could not be loaded for irsmsample.exe ******************************************************************************* * * * Exception Analysis * * * ******************************************************************************* TRIAGER: Could not open triage file : e:\dump_analysis\program\triage\guids.ini, error 2 TRIAGER: Could not open triage file : e:\dump_analysis\program\triage\modclass.ini, error 2 FAULTING_IP: mpich2!PMPI_Wtime+d9a6 0049a1c6 8b4804 mov ecx,dword ptr [eax+4] EXCEPTION_RECORD: ffffffff -- (.exr 0xffffffffffffffff) ExceptionAddress: 0049a1c6 (mpich2!PMPI_Wtime+0x0000d9a6) ExceptionCode: c0000005 (Access violation) ExceptionFlags: 00000000 NumberParameters: 2 Parameter[0]: 00000000 Parameter[1]: 00000004 Attempt to read from address 00000004 DEFAULT_BUCKET_ID: NULL_CLASS_PTR_READ PROCESS_NAME: irsmsample.exe ERROR_CODE: (NTSTATUS) 0xc0000005 - The instruction at "0x%08lx" referenced memory at "0x%08lx". The memory could not be "%s". EXCEPTION_CODE: (NTSTATUS) 0xc0000005 - The instruction at "0x%08lx" referenced memory at "0x%08lx". The memory could not be "%s". EXCEPTION_PARAMETER1: 00000000 EXCEPTION_PARAMETER2: 00000004 READ_ADDRESS: 00000004 FOLLOWUP_IP: mpich2!PMPI_Wtime+d9a6 0049a1c6 8b4804 mov ecx,dword ptr [eax+4] NTGLOBALFLAG: 0 APPLICATION_VERIFIER_FLAGS: 0 FAULTING_THREAD: 00000c0c PRIMARY_PROBLEM_CLASS: NULL_CLASS_PTR_READ BUGCHECK_STR: APPLICATION_FAULT_NULL_CLASS_PTR_READ LAST_CONTROL_TRANSFER: from 004013ae to 0049a1c6 STACK_TEXT: WARNING: Stack unwind information not available. Following frames may be wrong. 0012ff7c 004013ae 00000003 00384e20 00383a40 mpich2!PMPI_Wtime+0xd9a6 0012ffc0 7c817067 719c71e0 ffffffff 7ffd7000 irsmsample+0x13ae 0012fff0 00000000 00401555 00000000 00905a4d kernel32!BaseProcessStart+0x23 STACK_COMMAND: ~0s; .ecxr ; kb SYMBOL_STACK_INDEX: 0 SYMBOL_NAME: mpich2!PMPI_Wtime+d9a6 FOLLOWUP_NAME: MachineOwner MODULE_NAME: mpich2 IMAGE_NAME: mpich2.dll DEBUG_FLR_IMAGE_TIMESTAMP: 4e5fe70e FAILURE_BUCKET_ID: NULL_CLASS_PTR_READ_c0000005_mpich2.dll!PMPI_Wtime BUCKET_ID: APPLICATION_FAULT_NULL_CLASS_PTR_READ_mpich2!PMPI_Wtime+d9a6 WATSON_STAGEONE_URL: http://watson.microsoft.com/StageOne/irsmsample_exe/0_0_0_0/509d3866/mpich2… Followup: MachineOwner -----Message d'origine----- De : mpich-discuss-bounces(a)mcs.anl.gov [mailto:[email protected]] De la part de Calin Iaru Envoyé : jeudi 8 novembre 2012 11:05 À : mpich-discuss(a)mcs.anl.gov Objet : Re: [mpich-discuss] crash mpiexec This error code indicates an access violation inside MPI_Finalize(). I suggest you look at the core file. if(myid == 0) { struct rlimit rl; if(getrlimit(RLIMIT_CORE, &rl) == 0) { if(rl.rlim_cur == 0) { rl.rlim_cur = rl.rlim_max; setrlimit(RLIMIT_CORE,&rl); } } } From: NARDI Luigi Sent: Wednesday, November 07, 2012 2:08 PM To: mpich-discuss(a)mcs.anl.gov Subject: [mpich-discuss] crash mpiexec Hello, I have an error using mpiexec (MPICH2 1.4.1p). Hope somebody may help. The crash is random, i.e. the same executable may crash or not. Context: 5 nodes heterogeneous cluster: 4 nodes with CARMA (CUDA on ARM) on Ubuntu 11.4: the carrier board basically consists of an ARM Cortex A9 processor and a Quadro 1000M NVIDIA GPU card. 1 node with one XEON E5620 processor on Windows XP + cygwin. Standard Ethernet network. Names of the 5 nodes: lnardi carma1 carma2 carma3 carma4 The command line on the master node lnardi (Windows node) is: mpiexec -channel sock -n 1 -host lnardi a.out : -n 1 -host carma1 -path /home/lnardi/ a.out : -n 1 -host carma2 -path /home/lnardi/ a.out : -n 1 -host carma3 -path /home/lnardi/ a.out : -n 1 –host carma4 -path /home/lnardi/ a.out Notice that the same sample runs on a full linux cluster with the following characteristics: MVAPICH2-1.8a1p1 (mpirun) + MELLANOX infiniband + XEON X5675 + NVIDIA GPUs M2090 + Red Hat Enterprise Linux Server release 6.2. I was running a more complicated code but I have reproduced the error on a trivial code: #include <mpi.h> #include <stdio.h> #include <string.h> #define BUFSIZE 128 #define TAG 0 int main(int argc, char *argv[]) { char idstr[32]; char buff[BUFSIZE]; int numprocs; int myid; int i; MPI_Status stat; MPI_Init(&argc,&argv); MPI_Comm_size(MPI_COMM_WORLD,&numprocs); MPI_Comm_rank(MPI_COMM_WORLD,&myid); if(myid == 0) { printf("%d: We have %d processors\n", myid, numprocs); for(i=1;i<numprocs;i++) { sprintf(buff, "Hello %d! ", i); MPI_Send(buff, BUFSIZE, MPI_CHAR, i, TAG, MPI_COMM_WORLD); } for(i=1;i<numprocs;i++) { MPI_Recv(buff, BUFSIZE, MPI_CHAR, i, TAG, MPI_COMM_WORLD, &stat); printf("%d: %s\n", myid, buff); } } else { MPI_Recv(buff, BUFSIZE, MPI_CHAR, 0, TAG, MPI_COMM_WORLD, &stat); sprintf(idstr, "Processor %d ", myid); strncat(buff, idstr, BUFSIZE-1); strncat(buff, "reporting for duty\n", BUFSIZE-1); MPI_Send(buff, BUFSIZE, MPI_CHAR, 0, TAG, MPI_COMM_WORLD); } MPI_Finalize(); return 0; } The error: 0: We have 5 processors 0: Hello 1! Processor 1 reporting for duty 0: Hello 2! Processor 2 reporting for duty 0: Hello 3! Processor 3 reporting for duty 0: Hello 4! Processor 4 reporting for duty job aborted: rank: node: exit code[: error message] 0: lnardi: -1073741819: process 0 exited without calling finalize 1: carma1: -2 2: carma2: -2 3: carma3: -2 4: carma4: -2 I guess the problem comes from either the sock channel or mpiexec or ARM. What do you think about? Thanks Dr Luigi Nardi ******************************* This e-mail contains information for the intended recipient only. It may contain proprietary material or confidential information. If you are not the intended recipient you are not authorised to distribute, copy or use this e-mail or any attachment to it. Murex cannot guarantee that it is virus free and accepts no responsibility for any loss or damage arising from its use. If you have received this e-mail in error please notify immediately the sender and delete the original email received, any attachments and all copies from your system. _______________________________________________ mpich-discuss mailing list mpich-discuss(a)mcs.anl.gov To manage subscription options or unsubscribe: https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss _______________________________________________ mpich-discuss mailing list mpich-discuss(a)mcs.anl.gov To manage subscription options or unsubscribe: https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss ******************************* This e-mail contains information for the intended recipient only. It may contain proprietary material or confidential information. If you are not the intended recipient you are not authorised to distribute, copy or use this e-mail or any attachment to it. Murex cannot guarantee that it is virus free and accepts no responsibility for any loss or damage arising from its use. If you have received this e-mail in error please notify immediately the sender and delete the original email received, any attachments and all copies from your system.

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Compiler optimization flags in MPICH 3.0 rc1
by Yauheni Zelenko 15 Nov '12

15 Nov '12

Hi! I tried to build optimize and debug version of MPICH 3.0 rc1 and noticed some problems with compiler optimization flags. Looks like -O2 is set implicitly. For optimize configuration command like contains -O2 and -O3: ./configure --prefix=${InstallDir} \ --with-pm=hydra --with-device=ch3:nemesis \ --disable-chekpointing \ --enable-strict --enable-fast=O3 \ --disable-f77 --disable-fc \ CC=${GCCDir}/bin/gcc CFLAGS="-m32 -fPIC" \ CPP=${GCCDir}/bin/cpp \ CXX=${GCCDir}/bin/g++ CXXFLAGS="-m32 -fPIC" \ CXXCPP=${GCCDir}/bin/cpp For debug one -O2, but optimization is disabled: ./configure --prefix=${InstallDir} \ --with-pm=hydra --with-device=ch3:nemesis \ --disable-chekpointing \ --enable-strict --disable-fast -enable-g=debug \ --disable-f77 --disable-fc \ CC=${GCCDir}/bin/gcc CFLAGS="-m32 -fPIC" \ CPP=${GCCDir}/bin/cpp \ CXX=${GCCDir}/bin/g++ CXXFLAGS="-m32 -fPIC" \ CXXCPP=${GCCDir}/bin/cpp Eugene.

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Error when running
by Will Dixon 15 Nov '12

15 Nov '12

I am making a cluster for Francis Marion University and can't figure out how to get rid of this error. I understand what it is stating. A proxy is created but it can't find it once created. I think it isn't creating a proxy. The other errors seem to roll off errors from the proxy error. I tried looking up PMI but could find anything relative. I get this error every time I try to use mpirun -np 6 ./hello I have 6 ibook g3's that have powerpc processors and a headnode that is a tower that runs intel. I installed mpich2 on the headnode and on one of the slaves. I copied the slave's mpich to the others. I am able to ssh without any password to the slaves using rsa. my HYDRA_HOST_FILE environment variable is /mpich2/hosts [mpiexec@headnode] HYD_pmcd_pmiserv_proxy_init_cb (./pm/pmiserv/pmiserv_cb.c:529): cannot find proxy with ID 33554432 [mpiexec@headnode] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:77): callback returned error status [mpiexec@headnode] HYD_pmci_wait_for_completion (./pm/pmiserv/pmiserv_pmci.c:196): error waiting for event [mpiexec@headnode] main (./ui/mpich/mpiexec.c:325): process manager error waiting for completion I am able using c3 to run cexecs 'date' and they all return a date no problem. my /mpich2/hosts looks like: node01 node02 node03 node04 node05 node07 The headnode has two Ethernet ports one going to the internet and the other to a switch with the slaves connected to them. They are all running Debian Linux 6.0.6. Help would be much appreciated. Sincerely, Will Dixon

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Re: [mpich-discuss] mailing list issue
by Rajeev Thakur 14 Nov '12

14 Nov '12

Fixed. It should be https://lists.mpich.org/mailman/listinfo/discuss On Nov 14, 2012, at 2:52 PM, John Marshall wrote: > Hi, > > I sent an email to the discuss(a)mpich.org address and because I wasn't a member it > sent back: > You are not allowed to post to this mailing list because your email > address is not subscribed. Therefore, your message has been > automatically rejected. If you wish to subscribe to this list, please > do so at: > > > https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss > > > If you think that your messages are being rejected in error, please > check that you are using the correct email address when sending > messages, then contact the mailing list owner at > > mpich-discuss-owner(a)mcs.anl.gov > . > > The thing is, that mailman site does not have mpich-discuss. It should probably > redirect to: > https://lists.mpich.org/mailman/listinfo/mpich-discuss > or something like it, instead. > > John > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

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