June 2013 - discuss - mailman3.cels.anl.gov

Re: [mpich-discuss] discuss Digest, Vol 8, Issue 39
by Antonio J. Peña 24 Jun '13

24 Jun '13

Hi Jeff, Please correct me where I'm wrong: if only one thread calls MPI_Barrier, that one will get locked while others will go ahead. On the other hand, if every thread calls MPI_Barrier, all will get locked in that call until the barrier completes. That doesn't mean this will be a replacement for thread-wise synchronization mechanisms, but will be effective for all of them waiting for the barrier. Antonio On Monday, June 24, 2013 04:14:20 PM Jeff Hammond wrote: > MPI_Barrier will not sync threads. If N threads call MPI_Barrier, you will > get at best the same result as if you call MPI_Barrier N times from the > main thread. > > If you want to sync threads, you need to sync them with the appropriate > thread API. OpenMP and Pthreads both have barrier calls. If you want a > fast Pthread barrier, you should not use pthread_barrier though. The > Internet has details. > > Jeff > > ----- Original Message ----- > From: "Antonio J. Peña" <apenya(a)mcs.anl.gov> > To: discuss(a)mpich.org > Sent: Monday, June 24, 2013 3:49:08 PM > Subject: Re: [mpich-discuss] discuss Digest, Vol 8, Issue 39 > > > > > > > Sufeng, > > > > I'd say you're OK syncing your threads by all of them calling MPI_Barrier, > as it's a thread-safe function. > > > > Antonio > > > > > > On Monday, June 24, 2013 11:41:44 AM Sufeng Niu wrote: > > > Hi, Antonio > > > > Thanks a lot! Now I make sense. Let's say if I am running MPI and > multithreads program. If I called MPI_Barrier in each threads > > > what gonna happen? Will threads be synced by MPI_Barrier? or I should use > thread level sync? > > > > Thank you! > > > Sufeng > > > > > > > On Sun, Jun 23, 2013 at 6:54 PM, < discuss-request(a)mpich.org > wrote: > > > Send discuss mailing list submissions to > discuss(a)mpich.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.mpich.org/mailman/listinfo/discuss > or, via email, send a message with subject or body 'help' to > discuss-request(a)mpich.org > > You can reach the person managing the list at > discuss-owner(a)mpich.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of discuss digest..." > > > Today's Topics: > > 1. Re: Error with MPI_Spawn (Jeff Hammond) > 2. Re: discuss Digest, Vol 8, Issue 37 (Antonio J. Pe?a) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 23 Jun 2013 17:03:09 -0500 > From: Jeff Hammond < jeff.science(a)gmail.com > > To: " discuss(a)mpich.org " < discuss(a)mpich.org > > Subject: Re: [mpich-discuss] Error with MPI_Spawn > Message-ID: <-1578386667793986954@unknownmsgid> > Content-Type: text/plain; charset=ISO-8859-1 > > This is the wrong way to use PETSc and to parallelize a code with a > parallel library in general. > > Write the PETSc user list and they will explain to you how to > parallelize your code properly with PETSc. > > Jeff > > Sent from my iPhone > > On Jun 23, 2013, at 4:59 PM, Nitel Muhtaroglu < muhtaroglu.n(a)gmail.com > wrote: > > Hello, > > > > I am trying to integrate PETSc library to a serial program. The idea is > > that the serial program creates a linear equation system and then calls > > PETSc solver by MPI_Spawn and then solves this system in parallel. But > > when I execute MPI_Spawn the following error message occurs and the > > solver is not called. I couldn't find a solution to this error. Does > > anyone have an idea about it? > > > > Kind Regards, > > ------------------------------ > > Message: 2 > Date: Sun, 23 Jun 2013 18:54:38 -0500 > From: Antonio J. Pe?a < apenya(a)mcs.anl.gov > > To: discuss(a)mpich.org > Subject: Re: [mpich-discuss] discuss Digest, Vol 8, Issue 37 > Message-ID: <8872211.IGCl89YM8r(a)localhost.localdomain> > Content-Type: text/plain; charset="iso-8859-1" > > > Sufeng, > > The correct way is to use the MPI_Init_thread function with > MPI_THREAD_MULTIPLE. This will tell the MPI implementation to be thread > safe. It supports OpenMP and Posix Threads (OpenMP primitives in most > systems are likely to be implemented on top of PThreads). > > Antonio > > > On Sunday, June 23, 2013 11:13:31 AM Sufeng Niu wrote: > > > Hi, Antonio > > > Thanks a lot for your reply, I just figure out that is the firewall issue. > after I set the firewall. it works now. Thanks again. > > > But I still got a few questions on MPI and multithreads mixed programming. > Currently, I try to run each process on each server, and each process > using thread pool to run multiple threads (pthread lib). I am not sure > whether it is the correct way or not. I wrote it as: > > > MPI_Init() > .... > ... > /* create thread pool and initial */ > ...... > /* fetch job into thread pool */ > ...... > > > MPI_Finalize(); > > > When I check the book and notes, I found people use > > > MPI_Init_thread() with MPI_THREAD_MULTIPLE > > > but the some docs said it supported OpenMP, is that possible to use it > with pthread library? > I am new guy to this hybrid programming. I am not sure which is the proper > way to do it. Any suggestions are appreciate. Thank you! > > > Sufeng > > > > > On Sat, Jun 22, 2013 at 12:12 PM, < discuss-request(a)mpich.org [1]> wrote: > > > Send discuss mailing list submissions to discuss(a)mpich.org [2] > https://lists.mpich.org/mailman/listinfo/discuss[3] > discuss-request(a)mpich.org [1] > discuss-owner(a)mpich.org [4] > sniu(a)hawk.iit.edu [5]>To: discuss(a)mpich.org [2] > CAFNNHkwpqdGfZXctL0Uz3hpeL25mZZMtB93qGXjc_+tjnV4csA(a)mail.gmail.c > om[6]>Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > Sorry to bother you guys on this stupid question. last time I re-install > OSfor all blades to keep them the same version. after I mount, set > keylessssh, the terimnal gives the error below: > > [ proxy:0:[email protected] [7]] > HYDU_sock_connect(./utils/sock/sock.c:174): unable to connect from > " iocfccd3.aps.anl.gov [8]" to" iocfccd1.aps.anl.gov [9]" (No route to host) > [ proxy:0:[email protected] [7]] main (./pm/pmiserv/pmip.c:189): > unable toconnect to server iocfccd1.aps.anl.gov [9] at port 38242 (check > for firewalls!) > > I can ssh from iocfccd1 to iocfccd3 without password. Should I shut downall > firewalls on each server? I cannot find out where is the problem. Thankyou > > --Best Regards,Sufeng NiuECASP lab, ECE department, Illinois Institute of > TechnologyTel: 312-731-7219[10] > http://lists.mpich.org/pipermail/discuss/attachments/20130621/5503b1bc/a > ttachment-0001.html[11] > > > ------------------------------ > > Message: 2Date: Fri, 21 Jun 2013 10:58:26 -0500From: Antonio J. Pe?a > < apenya(a)mcs.anl.gov [12]>To: discuss(a)mpich.org [2] > iocfccd1.aps.anl.gov [9]" from iocfccd3?[1] > > Antonio > > > On Friday, June 21, 2013 10:51:50 AM Sufeng Niu wrote: > > > Hi, > > > Sorry to bother you guys on this stupid question. last time I re-install OS > forall blades to keep them the same version. after I mount, set keyless > ssh,the terimnal gives the error below: > > > proxy:0:[email protected] [7][2]] > HYDU_sock_connect(./utils/sock/sock.c:174): unable to connect from > " iocfccd3.aps.anl.gov [8][3]"to " iocfccd1.aps.anl.gov [9][1]" (No route to > host)[ proxy:0:[email protected] [7][2]] main > (./pm/pmiserv/pmip.c:189):unable to connect to server > iocfccd1.aps.anl.gov [9][1] at port 38242 (checkfor firewalls!) > > > > I can ssh from iocfccd1 to iocfccd3 without password. Should I shut downall > firewalls on each server? I cannot find out where is the problem. Thankyou > > > > > -- Best Regards,Sufeng NiuECASP lab, ECE department, Illinois Institute of > TechnologyTel: 312-731-7219[4] > > > --------[1] _ http://iocfccd1.aps.anl.gov_ > proxy%3A0%3A1(a)iocfccd3.aps.anl.gov [13] > http://iocfccd3.aps.anl.gov [8] > 312-731-7219[10] > http://lists.mpich.org/pipermail/discuss/attachments/20130621/01b37902/ > attachment-0001.html[14] > > > ------------------------------ > > Message: 3Date: Sat, 22 Jun 2013 12:49:10 -0400From: Jiri Simsa > < jsimsa(a)cs.cmu.edu [15]>To: discuss(a)mpich.org [2] > CAHs9ut-_6W6SOHTJ_rD+shQ76bo4cTCuFVAy1f9x- > J0gioakHg(a)mail.gmail.com [16]>Content-Type: text/plain; > charset="iso-8859-1" > > Hi, >

1 0

Re: [mpich-discuss] discuss Digest, Vol 8, Issue 39
by Jeff Hammond 24 Jun '13

24 Jun '13

MPI_Barrier will not sync threads. If N threads call MPI_Barrier, you will get at best the same result as if you call MPI_Barrier N times from the main thread. If you want to sync threads, you need to sync them with the appropriate thread API. OpenMP and Pthreads both have barrier calls. If you want a fast Pthread barrier, you should not use pthread_barrier though. The Internet has details. Jeff ----- Original Message ----- From: "Antonio J. Peña" <apenya(a)mcs.anl.gov> To: discuss(a)mpich.org Sent: Monday, June 24, 2013 3:49:08 PM Subject: Re: [mpich-discuss] discuss Digest, Vol 8, Issue 39 Sufeng, I'd say you're OK syncing your threads by all of them calling MPI_Barrier, as it's a thread-safe function. Antonio On Monday, June 24, 2013 11:41:44 AM Sufeng Niu wrote: Hi, Antonio Thanks a lot! Now I make sense. Let's say if I am running MPI and multithreads program. If I called MPI_Barrier in each threads what gonna happen? Will threads be synced by MPI_Barrier? or I should use thread level sync? Thank you! Sufeng On Sun, Jun 23, 2013 at 6:54 PM, < discuss-request(a)mpich.org > wrote: Send discuss mailing list submissions to discuss(a)mpich.org To subscribe or unsubscribe via the World Wide Web, visit https://lists.mpich.org/mailman/listinfo/discuss or, via email, send a message with subject or body 'help' to discuss-request(a)mpich.org You can reach the person managing the list at discuss-owner(a)mpich.org When replying, please edit your Subject line so it is more specific than "Re: Contents of discuss digest..." Today's Topics: 1. Re: Error with MPI_Spawn (Jeff Hammond) 2. Re: discuss Digest, Vol 8, Issue 37 (Antonio J. Pe?a) ---------------------------------------------------------------------- Message: 1 Date: Sun, 23 Jun 2013 17:03:09 -0500 From: Jeff Hammond < jeff.science(a)gmail.com > To: " discuss(a)mpich.org " < discuss(a)mpich.org > Subject: Re: [mpich-discuss] Error with MPI_Spawn Message-ID: <-1578386667793986954@unknownmsgid> Content-Type: text/plain; charset=ISO-8859-1 This is the wrong way to use PETSc and to parallelize a code with a parallel library in general. Write the PETSc user list and they will explain to you how to parallelize your code properly with PETSc. Jeff Sent from my iPhone On Jun 23, 2013, at 4:59 PM, Nitel Muhtaroglu < muhtaroglu.n(a)gmail.com > wrote: > Hello, > > I am trying to integrate PETSc library to a serial program. The idea is that the serial program creates a linear equation system and then calls PETSc solver by MPI_Spawn and then solves this system in parallel. But when I execute MPI_Spawn the following error message occurs and the solver is not called. I couldn't find a solution to this error. Does anyone have an idea about it? > > Kind Regards, > -- > Nitel > > ********************************************************** > Assertion failed in file socksm.c at line 590: hdr.pkt_type == MPIDI_NEM_TCP_SOCKSM_PKT_ID_INFO || hdr.pkt_type == MPIDI_NEM_TCP_SOCKSM_PKT_TMPVC_INFO > internal ABORT - process 0 > INTERNAL ERROR: Invalid error class (66) encountered while returning from > MPI_Init. Please file a bug report. > Fatal error in MPI_Init: Unknown error. Please file a bug report., error stack: > (unknown)(): connection failure > [cli_0]: aborting job: > Fatal error in MPI_Init: Unknown error. Please file a bug report., error stack: > (unknown)(): connection failure > ********************************************************** > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss ------------------------------ Message: 2 Date: Sun, 23 Jun 2013 18:54:38 -0500 From: Antonio J. Pe?a < apenya(a)mcs.anl.gov > To: discuss(a)mpich.org Subject: Re: [mpich-discuss] discuss Digest, Vol 8, Issue 37 Message-ID: <8872211.IGCl89YM8r(a)localhost.localdomain> Content-Type: text/plain; charset="iso-8859-1" Sufeng, The correct way is to use the MPI_Init_thread function with MPI_THREAD_MULTIPLE. This will tell the MPI implementation to be thread safe. It supports OpenMP and Posix Threads (OpenMP primitives in most systems are likely to be implemented on top of PThreads). Antonio On Sunday, June 23, 2013 11:13:31 AM Sufeng Niu wrote: Hi, Antonio Thanks a lot for your reply, I just figure out that is the firewall issue. after I set the firewall. it works now. Thanks again. But I still got a few questions on MPI and multithreads mixed programming. Currently, I try to run each process on each server, and each process using thread pool to run multiple threads (pthread lib). I am not sure whether it is the correct way or not. I wrote it as: MPI_Init() .... ... /* create thread pool and initial */ ...... /* fetch job into thread pool */ ...... MPI_Finalize(); When I check the book and notes, I found people use MPI_Init_thread() with MPI_THREAD_MULTIPLE but the some docs said it supported OpenMP, is that possible to use it with pthread library? I am new guy to this hybrid programming. I am not sure which is the proper way to do it. Any suggestions are appreciate. Thank you! Sufeng On Sat, Jun 22, 2013 at 12:12 PM, < discuss-request(a)mpich.org [1]> wrote: Send discuss mailing list submissions to discuss(a)mpich.org [2] https://lists.mpich.org/mailman/listinfo/discuss[3] discuss-request(a)mpich.org [1] discuss-owner(a)mpich.org [4] sniu(a)hawk.iit.edu [5]>To: discuss(a)mpich.org [2] CAFNNHkwpqdGfZXctL0Uz3hpeL25mZZMtB93qGXjc_+tjnV4csA(a)mail.gmail.c om[6]>Content-Type: text/plain; charset="iso-8859-1" Hi, Sorry to bother you guys on this stupid question. last time I re-install OSfor all blades to keep them the same version. after I mount, set keylessssh, the terimnal gives the error below: [ proxy:0:[email protected] [7]] HYDU_sock_connect(./utils/sock/sock.c:174): unable to connect from " iocfccd3.aps.anl.gov [8]" to" iocfccd1.aps.anl.gov [9]" (No route to host) [ proxy:0:[email protected] [7]] main (./pm/pmiserv/pmip.c:189): unable toconnect to server iocfccd1.aps.anl.gov [9] at port 38242 (check for firewalls!) I can ssh from iocfccd1 to iocfccd3 without password. Should I shut downall firewalls on each server? I cannot find out where is the problem. Thankyou --Best Regards,Sufeng NiuECASP lab, ECE department, Illinois Institute of TechnologyTel: 312-731-7219[10] http://lists.mpich.org/pipermail/discuss/attachments/20130621/5503b1bc/a ttachment-0001.html[11] > ------------------------------ Message: 2Date: Fri, 21 Jun 2013 10:58:26 -0500From: Antonio J. Pe?a < apenya(a)mcs.anl.gov [12]>To: discuss(a)mpich.org [2] iocfccd1.aps.anl.gov [9]" from iocfccd3?[1] Antonio On Friday, June 21, 2013 10:51:50 AM Sufeng Niu wrote: Hi, Sorry to bother you guys on this stupid question. last time I re-install OS forall blades to keep them the same version. after I mount, set keyless ssh,the terimnal gives the error below: proxy:0:[email protected] [7][2]] HYDU_sock_connect(./utils/sock/sock.c:174): unable to connect from " iocfccd3.aps.anl.gov [8][3]"to " iocfccd1.aps.anl.gov [9][1]" (No route to host)[ proxy:0:[email protected] [7][2]] main (./pm/pmiserv/pmip.c:189):unable to connect to server iocfccd1.aps.anl.gov [9][1] at port 38242 (checkfor firewalls!) I can ssh from iocfccd1 to iocfccd3 without password. Should I shut downall firewalls on each server? I cannot find out where is the problem. Thankyou -- Best Regards,Sufeng NiuECASP lab, ECE department, Illinois Institute of TechnologyTel: 312-731-7219[4] --------[1] _ http://iocfccd1.aps.anl.gov_ proxy%3A0%3A1(a)iocfccd3.aps.anl.gov [13] http://iocfccd3.aps.anl.gov [8] 312-731-7219[10] http://lists.mpich.org/pipermail/discuss/attachments/20130621/01b37902/ attachment-0001.html[14] > ------------------------------ Message: 3Date: Sat, 22 Jun 2013 12:49:10 -0400From: Jiri Simsa < jsimsa(a)cs.cmu.edu [15]>To: discuss(a)mpich.org [2] CAHs9ut-_6W6SOHTJ_rD+shQ76bo4cTCuFVAy1f9x- J0gioakHg(a)mail.gmail.com [16]>Content-Type: text/plain; charset="iso-8859-1" Hi, -------------- next part -------------- An HTML attachment was scrubbed... URL: < http://lists.mpich.org/pipermail/discuss/attachments/20130623/a6104115/atta… > ------------------------------ _______________________________________________ discuss mailing list discuss(a)mpich.org https://lists.mpich.org/mailman/listinfo/discuss End of discuss Digest, Vol 8, Issue 39 ************************************** -- Best Regards, Sufeng Niu ECASP lab, ECE department, Illinois Institute of Technology Tel: 312-731-7219 -- Antonio J. Peña Postdoctoral Appointee Mathematics and Computer Science Division Argonne National Laboratory 9700 South Cass Avenue, Bldg. 240, Of. 3148 Argonne, IL 60439-4847 (+1) 630-252-7928 apenya(a)mcs.anl.gov _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

1 0

Re: [mpich-discuss] discuss Digest, Vol 8, Issue 39
by Antonio J. Peña 24 Jun '13

24 Jun '13

Sufeng, I'd say you're OK syncing your threads by all of them calling MPI_Barrier, as it's a thread-safe function. Antonio On Monday, June 24, 2013 11:41:44 AM Sufeng Niu wrote: Hi, Antonio Thanks a lot! Now I make sense. Let's say if I am running MPI and multithreads program. If I called MPI_Barrier in each threads what gonna happen? Will threads be synced by MPI_Barrier? or I should use thread level sync? Thank you! Sufeng On Sun, Jun 23, 2013 at 6:54 PM, <discuss-request(a)mpich.org[1]> wrote: Send discuss mailing list submissions to discuss(a)mpich.org[2] https://lists.mpich.org/mailman/listinfo/discuss[3] discuss-request(a)mpich.org[1] discuss-owner(a)mpich.org[4] jeff.science(a)gmail.com[5]>To: "discuss(a)mpich.org[2]" <_discuss(a)mpich.org_>Subject: Re: [mpich-discuss] Error with MPI_SpawnMessage-ID: <-1578386667793986954@unknownmsgid>Content-Type: text/plain; charset=ISO-8859-1 This is the wrong way to use PETSc and to parallelize a code with aparallel library in general. Write the PETSc user list and they will explain to you how toparallelize your code properly with PETSc. Jeff Sent from my iPhone On Jun 23, 2013, at 4:59 PM, Nitel Muhtaroglu <muhtaroglu.n(a)gmail.com[6]> wrote: > Hello,>> I am trying to integrate PETSc library to a serial program. The idea is that the serial program creates a linear equation system and then calls PETSc solver by MPI_Spawn and then solves this system in parallel. But when I execute MPI_Spawn the following error message occurs and the solver is not called. I couldn't find a solution to this error. Does anyone have an idea about it?>> Kind Regards,> --> Nitel>> **********************************************************> Assertion failed in file socksm.c at line 590: hdr.pkt_type == MPIDI_NEM_TCP_SOCKSM_PKT_ID_INFO || hdr.pkt_type == MPIDI_NEM_TCP_SOCKSM_PKT_TMPVC_INFO> internal ABORT - process 0> INTERNAL ERROR: Invalid error class (66) encountered while returning from> MPI_Init. Please file a bug report.> Fatal error in MPI_Init: Unknown error. Please file a bug report., error stack:> (unknown)(): connection failure> [cli_0]: aborting job:> Fatal error in MPI_Init: Unknown error. Please file a bug report., error stack:> (unknown)(): connection failure> **********************************************************> _______________________________________________> discuss mailing list discuss(a)mpich.org[2] https://lists.mpich.org/mailman/listinfo/discuss[3] apenya(a)mcs.anl.gov[7]>To: discuss(a)mpich.org[2] discuss-request(a)mpich.org[1][1]> wrote: Send discuss mailing list submissions to discuss(a)mpich.org[2][2] https://lists.mpich.org/mailman/listinfo/discuss[3][8] discuss-request(a)mpich.org[1][1] discuss-owner(a)mpich.org[4][4] sniu(a)hawk.iit.edu[9][5]>To: discuss(a)mpich.org[2] [2]CAFNNHkwpqdGfZXctL0Uz3hpeL25mZZMtB93qGXjc_+tjnV4csA(a)mail.gma il.com[6]>Content-Type: text/plain; charset="iso-8859-1" Hi, Sorry to bother you guys on this stupid question. last time I re-install OSforall blades to keep them the same version. after I mount, set keylessssh,the terimnal gives the error below: [proxy:0:[email protected][10] [7]]HYDU_sock_connect(./utils/sock/sock.c:174): unable to connect from"iocfccd3.aps.anl.gov[11][8]" to"iocfccd1.aps.anl.gov[12][9]" (No route to host)[proxy:0:[email protected][10][7]] main (./pm/pmiserv/pmip.c:189):unable toconnect to server iocfccd1.aps.anl.gov[12][9] at port 38242 (checkfor firewalls!) I can ssh from iocfccd1 to iocfccd3 without password. Should I shut downallfirewalls on each server? I cannot find out where is the problem. Thankyou --Best Regards,Sufeng NiuECASP lab, ECE department, Illinois Institute ofTechnologyTel: 312-731-7219[10] http://lists.mpich.org/pipermail/discuss/attachments/20130621/5503b1bc/a ttachment-0001.html[11][13]> ------------------------------ Message: 2Date: Fri, 21 Jun 2013 10:58:26 -0500From: Antonio J. Pe?a<apenya(a)mcs.anl.gov[7][12]>To: discuss(a)mpich.org[2][2] iocfccd1.aps.anl.gov[12][9]" from iocfccd3?[1] Antonio On Friday, June 21, 2013 10:51:50 AM Sufeng Niu wrote: Hi, Sorry to bother you guys on this stupid question. last time I re-install OSforall blades to keep them the same version. after I mount, set keylessssh,the terimnal gives the error below: proxy:0:[email protected][10][7] [2]]HYDU_sock_connect(./utils/sock/sock.c:174): unable to connect from"iocfccd3.aps.anl.gov[11][8][3]"to "iocfccd1.aps.anl.gov[12][9][1]" (No route tohost)[proxy:0:[email protected][10][7][2]] main(./pm/pmiserv/pmip.c:189):unable to connect to server

1 0

Problem with ADIOI_Info_get (MPI_Info_get) from the ADIO layer
by Matthieu Dorier 24 Jun '13

24 Jun '13

Hi, I'm implementing an ADIO backend and I'm having problems retrieving values from the MPI_Info attached to the file. On the application side, I have something like this: MPI_Info_create(&info); MPI_Info_set(info,"cb_buffer_size","64"); MPI_Info_set(info,"xyz","3"); MPI_File_open(comm, "file", MPI_MODE_WRONLY | MPI_MODE_CREATE, info, &fh); then a call to a MPI_File_write, which ends up calling my implementation of ADIOI_xxx_WriteContig. In this function, I try to read back these info: int info_flag; char* value = (char *) ADIOI_Malloc((MPI_MAX_INFO_VAL+1)*sizeof(char)); ADIOI_Info_get(fd->info, "xyz", MPI_MAX_INFO_VAL, value,&info_flag); if(info_flag) fprintf(stderr,"xyz = %d\n",atoi(value)); ADIOI_Info_get(fd->info, "cb_buffer_size", MPI_MAX_INFO_VAL, value,&info_flag); if(info_flag) fprintf(stderr,"cb_buffer_size = %d\n",atoi(value)); I can get the 64 associated to the cb_buffer_size key (which is a reserved hint), but I don't get the second value. Where does the problem come from? I tried everything: re-ordering the calls, changing the name of the key, calling MPI_Info_get in the application to check that the values are properly set (they are)... Thanks Matthieu Dorier PhD student at ENS Cachan Brittany and IRISA http://people.irisa.fr/Matthieu.Dorier

1 0

Re: [mpich-discuss] discuss Digest, Vol 8, Issue 39
by Sufeng Niu 24 Jun '13

24 Jun '13

Hi, Antonio Thanks a lot! Now I make sense. Let's say if I am running MPI and multithreads program. If I called MPI_Barrier in each threads what gonna happen? Will threads be synced by MPI_Barrier? or I should use thread level sync? Thank you! Sufeng On Sun, Jun 23, 2013 at 6:54 PM, <discuss-request(a)mpich.org> wrote: > Send discuss mailing list submissions to > discuss(a)mpich.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.mpich.org/mailman/listinfo/discuss > or, via email, send a message with subject or body 'help' to > discuss-request(a)mpich.org > > You can reach the person managing the list at > discuss-owner(a)mpich.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of discuss digest..." > > > Today's Topics: > > 1. Re: Error with MPI_Spawn (Jeff Hammond) > 2. Re: discuss Digest, Vol 8, Issue 37 (Antonio J. Pe?a) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 23 Jun 2013 17:03:09 -0500 > From: Jeff Hammond <jeff.science(a)gmail.com> > To: "discuss(a)mpich.org" <discuss(a)mpich.org> > Subject: Re: [mpich-discuss] Error with MPI_Spawn > Message-ID: <-1578386667793986954@unknownmsgid> > Content-Type: text/plain; charset=ISO-8859-1 > > This is the wrong way to use PETSc and to parallelize a code with a > parallel library in general. > > Write the PETSc user list and they will explain to you how to > parallelize your code properly with PETSc. > > Jeff > > Sent from my iPhone > > On Jun 23, 2013, at 4:59 PM, Nitel Muhtaroglu <muhtaroglu.n(a)gmail.com> > wrote: > > > Hello, > > > > I am trying to integrate PETSc library to a serial program. The idea is > that the serial program creates a linear equation system and then calls > PETSc solver by MPI_Spawn and then solves this system in parallel. But when > I execute MPI_Spawn the following error message occurs and the solver is > not called. I couldn't find a solution to this error. Does anyone have an > idea about it? > > > > Kind Regards, > > -- > > Nitel > > > > ********************************************************** > > Assertion failed in file socksm.c at line 590: hdr.pkt_type == > MPIDI_NEM_TCP_SOCKSM_PKT_ID_INFO || hdr.pkt_type == > MPIDI_NEM_TCP_SOCKSM_PKT_TMPVC_INFO > > internal ABORT - process 0 > > INTERNAL ERROR: Invalid error class (66) encountered while returning from > > MPI_Init. Please file a bug report. > > Fatal error in MPI_Init: Unknown error. Please file a bug report., > error stack: > > (unknown)(): connection failure > > [cli_0]: aborting job: > > Fatal error in MPI_Init: Unknown error. Please file a bug report., > error stack: > > (unknown)(): connection failure > > ********************************************************** > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > ------------------------------ > > Message: 2 > Date: Sun, 23 Jun 2013 18:54:38 -0500 > From: Antonio J. Pe?a <apenya(a)mcs.anl.gov> > To: discuss(a)mpich.org > Subject: Re: [mpich-discuss] discuss Digest, Vol 8, Issue 37 > Message-ID: <8872211.IGCl89YM8r(a)localhost.localdomain> > Content-Type: text/plain; charset="iso-8859-1" > > > Sufeng, > > The correct way is to use the MPI_Init_thread function with > MPI_THREAD_MULTIPLE. This will tell the MPI implementation to be thread > safe. It supports OpenMP and Posix Threads (OpenMP primitives in most > systems are likely to be implemented on top of PThreads). > > Antonio > > > On Sunday, June 23, 2013 11:13:31 AM Sufeng Niu wrote: > > > Hi, Antonio > > > Thanks a lot for your reply, I just figure out that is the firewall issue. > after I > set the firewall. it works now. Thanks again. > > > But I still got a few questions on MPI and multithreads mixed programming. > Currently, I try to run each process on each server, and each process > using thread pool to run multiple threads (pthread lib). I am not sure > whether it is the correct way or not. I wrote it as: > > > MPI_Init() > .... > ... > /* create thread pool and initial */ > ...... > /* fetch job into thread pool */ > ...... > > > MPI_Finalize(); > > > When I check the book and notes, I found people use > > > MPI_Init_thread() with MPI_THREAD_MULTIPLE > > > but the some docs said it supported OpenMP, is that possible to use it > with pthread library? > I am new guy to this hybrid programming. I am not sure which is the proper > way to do it. Any suggestions are appreciate. Thank you! > > > Sufeng > > > > > On Sat, Jun 22, 2013 at 12:12 PM, <discuss-request(a)mpich.org[1]> wrote: > > > Send discuss mailing list submissions to discuss(a)mpich.org[2] > https://lists.mpich.org/mailman/listinfo/discuss[3] > discuss-request(a)mpich.org[1] > discuss-owner(a)mpich.org[4] > sniu(a)hawk.iit.edu[5]>To: discuss(a)mpich.org[2] > CAFNNHkwpqdGfZXctL0Uz3hpeL25mZZMtB93qGXjc_+tjnV4csA(a)mail.gmail.c > om[6]>Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > Sorry to bother you guys on this stupid question. last time I re-install > OSfor > all blades to keep them the same version. after I mount, set keylessssh, > the terimnal gives the error below: > > [proxy:0:[email protected][7]] > HYDU_sock_connect(./utils/sock/sock.c:174): unable to connect from > "iocfccd3.aps.anl.gov[8]" to"iocfccd1.aps.anl.gov[9]" (No route to host) > [proxy:0:[email protected][7]] main (./pm/pmiserv/pmip.c:189): > unable toconnect to server iocfccd1.aps.anl.gov[9] at port 38242 (check > for firewalls!) > > I can ssh from iocfccd1 to iocfccd3 without password. Should I shut downall > firewalls on each server? I cannot find out where is the problem. Thankyou > > --Best Regards,Sufeng NiuECASP lab, ECE department, Illinois Institute of > TechnologyTel: 312-731-7219[10] > http://lists.mpich.org/pipermail/discuss/attachments/20130621/5503b1bc/a > ttachment-0001.html[11]> > > ------------------------------ > > Message: 2Date: Fri, 21 Jun 2013 10:58:26 -0500From: Antonio J. Pe?a > <apenya(a)mcs.anl.gov[12]>To: discuss(a)mpich.org[2] > iocfccd1.aps.anl.gov[9]" from iocfccd3?[1] > > Antonio > > > On Friday, June 21, 2013 10:51:50 AM Sufeng Niu wrote: > > > Hi, > > > Sorry to bother you guys on this stupid question. last time I re-install OS > forall blades to keep them the same version. after I mount, set keyless > ssh,the terimnal gives the error below: > > > proxy:0:[email protected][7][2]] > HYDU_sock_connect(./utils/sock/sock.c:174): unable to connect from > "iocfccd3.aps.anl.gov[8][3]"to "iocfccd1.aps.anl.gov[9][1]" (No route to > host)[proxy:0:[email protected][7][2]] main > (./pm/pmiserv/pmip.c:189):unable to connect to server > iocfccd1.aps.anl.gov[9][1] at port 38242 (checkfor firewalls!) > > > > I can ssh from iocfccd1 to iocfccd3 without password. Should I shut downall > firewalls on each server? I cannot find out where is the problem. Thankyou > > > > > -- Best Regards,Sufeng NiuECASP lab, ECE department, Illinois Institute of > TechnologyTel: 312-731-7219[4] > > > --------[1] _http://iocfccd1.aps.anl.gov_ > proxy%3A0%3A1(a)iocfccd3.aps.anl.gov[13] > http://iocfccd3.aps.anl.gov[8] > 312-731-7219[10] > http://lists.mpich.org/pipermail/discuss/attachments/20130621/01b37902/ > attachment-0001.html[14]> > > ------------------------------ > > Message: 3Date: Sat, 22 Jun 2013 12:49:10 -0400From: Jiri Simsa > <jsimsa(a)cs.cmu.edu[15]>To: discuss(a)mpich.org[2] > CAHs9ut-_6W6SOHTJ_rD+shQ76bo4cTCuFVAy1f9x- > J0gioakHg(a)mail.gmail.com[16]>Content-Type: text/plain; > charset="iso-8859-1" > > Hi, >

1 0

Re: [mpich-discuss] discuss Digest, Vol 8, Issue 37
by Antonio J. Peña 23 Jun '13

23 Jun '13

Sufeng, The correct way is to use the MPI_Init_thread function with MPI_THREAD_MULTIPLE. This will tell the MPI implementation to be thread safe. It supports OpenMP and Posix Threads (OpenMP primitives in most systems are likely to be implemented on top of PThreads). Antonio On Sunday, June 23, 2013 11:13:31 AM Sufeng Niu wrote: Hi, Antonio Thanks a lot for your reply, I just figure out that is the firewall issue. after I set the firewall. it works now. Thanks again. But I still got a few questions on MPI and multithreads mixed programming. Currently, I try to run each process on each server, and each process using thread pool to run multiple threads (pthread lib). I am not sure whether it is the correct way or not. I wrote it as: MPI_Init() .... ... /* create thread pool and initial */ ...... /* fetch job into thread pool */ ...... MPI_Finalize(); When I check the book and notes, I found people use MPI_Init_thread() with MPI_THREAD_MULTIPLE but the some docs said it supported OpenMP, is that possible to use it with pthread library? I am new guy to this hybrid programming. I am not sure which is the proper way to do it. Any suggestions are appreciate. Thank you! Sufeng On Sat, Jun 22, 2013 at 12:12 PM, <discuss-request(a)mpich.org[1]> wrote: Send discuss mailing list submissions to discuss(a)mpich.org[2] https://lists.mpich.org/mailman/listinfo/discuss[3] discuss-request(a)mpich.org[1] discuss-owner(a)mpich.org[4] sniu(a)hawk.iit.edu[5]>To: discuss(a)mpich.org[2] CAFNNHkwpqdGfZXctL0Uz3hpeL25mZZMtB93qGXjc_+tjnV4csA(a)mail.gmail.c om[6]>Content-Type: text/plain; charset="iso-8859-1" Hi, Sorry to bother you guys on this stupid question. last time I re-install OSfor all blades to keep them the same version. after I mount, set keylessssh, the terimnal gives the error below: [proxy:0:[email protected][7]] HYDU_sock_connect(./utils/sock/sock.c:174): unable to connect from "iocfccd3.aps.anl.gov[8]" to"iocfccd1.aps.anl.gov[9]" (No route to host) [proxy:0:[email protected][7]] main (./pm/pmiserv/pmip.c:189): unable toconnect to server iocfccd1.aps.anl.gov[9] at port 38242 (check for firewalls!) I can ssh from iocfccd1 to iocfccd3 without password. Should I shut downall firewalls on each server? I cannot find out where is the problem. Thankyou --Best Regards,Sufeng NiuECASP lab, ECE department, Illinois Institute of TechnologyTel: 312-731-7219[10] http://lists.mpich.org/pipermail/discuss/attachments/20130621/5503b1bc/a ttachment-0001.html[11]> ------------------------------ Message: 2Date: Fri, 21 Jun 2013 10:58:26 -0500From: Antonio J. Pe?a <apenya(a)mcs.anl.gov[12]>To: discuss(a)mpich.org[2] iocfccd1.aps.anl.gov[9]" from iocfccd3?[1] Antonio On Friday, June 21, 2013 10:51:50 AM Sufeng Niu wrote: Hi, Sorry to bother you guys on this stupid question. last time I re-install OS forall blades to keep them the same version. after I mount, set keyless ssh,the terimnal gives the error below: proxy:0:[email protected][7][2]] HYDU_sock_connect(./utils/sock/sock.c:174): unable to connect from "iocfccd3.aps.anl.gov[8][3]"to "iocfccd1.aps.anl.gov[9][1]" (No route to host)[proxy:0:[email protected][7][2]] main (./pm/pmiserv/pmip.c:189):unable to connect to server iocfccd1.aps.anl.gov[9][1] at port 38242 (checkfor firewalls!) I can ssh from iocfccd1 to iocfccd3 without password. Should I shut downall firewalls on each server? I cannot find out where is the problem. Thankyou -- Best Regards,Sufeng NiuECASP lab, ECE department, Illinois Institute of TechnologyTel: 312-731-7219[4] --------[1] _http://iocfccd1.aps.anl.gov_ proxy%3A0%3A1(a)iocfccd3.aps.anl.gov[13] http://iocfccd3.aps.anl.gov[8] 312-731-7219[10] http://lists.mpich.org/pipermail/discuss/attachments/20130621/01b37902/ attachment-0001.html[14]> ------------------------------ Message: 3Date: Sat, 22 Jun 2013 12:49:10 -0400From: Jiri Simsa <jsimsa(a)cs.cmu.edu[15]>To: discuss(a)mpich.org[2] CAHs9ut-_6W6SOHTJ_rD+shQ76bo4cTCuFVAy1f9x- J0gioakHg(a)mail.gmail.com[16]>Content-Type: text/plain; charset="iso-8859-1" Hi,

1 0

Re: [mpich-discuss] Error with MPI_Spawn
by Jeff Hammond 23 Jun '13

23 Jun '13

This is the wrong way to use PETSc and to parallelize a code with a parallel library in general. Write the PETSc user list and they will explain to you how to parallelize your code properly with PETSc. Jeff Sent from my iPhone On Jun 23, 2013, at 4:59 PM, Nitel Muhtaroglu <muhtaroglu.n(a)gmail.com> wrote: > Hello, > > I am trying to integrate PETSc library to a serial program. The idea is that the serial program creates a linear equation system and then calls PETSc solver by MPI_Spawn and then solves this system in parallel. But when I execute MPI_Spawn the following error message occurs and the solver is not called. I couldn't find a solution to this error. Does anyone have an idea about it? > > Kind Regards, > -- > Nitel > > ********************************************************** > Assertion failed in file socksm.c at line 590: hdr.pkt_type == MPIDI_NEM_TCP_SOCKSM_PKT_ID_INFO || hdr.pkt_type == MPIDI_NEM_TCP_SOCKSM_PKT_TMPVC_INFO > internal ABORT - process 0 > INTERNAL ERROR: Invalid error class (66) encountered while returning from > MPI_Init. Please file a bug report. > Fatal error in MPI_Init: Unknown error. Please file a bug report., error stack: > (unknown)(): connection failure > [cli_0]: aborting job: > Fatal error in MPI_Init: Unknown error. Please file a bug report., error stack: > (unknown)(): connection failure > ********************************************************** > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

1 0

Error with MPI_Spawn
by Nitel Muhtaroglu 23 Jun '13

23 Jun '13

Hello, I am trying to integrate PETSc library to a serial program. The idea is that the serial program creates a linear equation system and then calls PETSc solver by MPI_Spawn and then solves this system in parallel. But when I execute MPI_Spawn the following error message occurs and the solver is not called. I couldn't find a solution to this error. Does anyone have an idea about it? Kind Regards, -- Nitel ********************************************************** Assertion failed in file socksm.c at line 590: hdr.pkt_type == MPIDI_NEM_TCP_SOCKSM_PKT_ID_INFO || hdr.pkt_type == MPIDI_NEM_TCP_SOCKSM_PKT_TMPVC_INFO internal ABORT - process 0 INTERNAL ERROR: Invalid error class (66) encountered while returning from MPI_Init. Please file a bug report. Fatal error in MPI_Init: Unknown error. Please file a bug report., error stack: (unknown)(): connection failure [cli_0]: aborting job: Fatal error in MPI_Init: Unknown error. Please file a bug report., error stack: (unknown)(): connection failure **********************************************************

1 0

Re: [mpich-discuss] discuss Digest, Vol 8, Issue 37
by Sufeng Niu 23 Jun '13

23 Jun '13

Hi, Antonio Thanks a lot for your reply, I just figure out that is the firewall issue. after I set the firewall. it works now. Thanks again. But I still got a few questions on MPI and multithreads mixed programming. Currently, I try to run each process on each server, and each process using thread pool to run multiple threads (pthread lib). I am not sure whether it is the correct way or not. I wrote it as: MPI_Init() .... ... /* create thread pool and initial */ ...... /* fetch job into thread pool */ ...... MPI_Finalize(); When I check the book and notes, I found people use MPI_Init_thread() with MPI_THREAD_MULTIPLE but the some docs said it supported OpenMP, is that possible to use it with pthread library? I am new guy to this hybrid programming. I am not sure which is the proper way to do it. Any suggestions are appreciate. Thank you! Sufeng On Sat, Jun 22, 2013 at 12:12 PM, <discuss-request(a)mpich.org> wrote: > Send discuss mailing list submissions to > discuss(a)mpich.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.mpich.org/mailman/listinfo/discuss > or, via email, send a message with subject or body 'help' to > discuss-request(a)mpich.org > > You can reach the person managing the list at > discuss-owner(a)mpich.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of discuss digest..." > > > Today's Topics: > > 1. run hello world on multiple server (Sufeng Niu) > 2. Re: run hello world on multiple server (Antonio J. Pe?a) > 3. Problem reproducing an example from the MPI standard (Jiri Simsa) > 4. Re: Problem reproducing an example from the MPI standard > (Pavan Balaji) > 5. Re: Problem reproducing an example from the MPI standard > (Jiri Simsa) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 21 Jun 2013 10:51:50 -0500 > From: Sufeng Niu <sniu(a)hawk.iit.edu> > To: discuss(a)mpich.org > Subject: [mpich-discuss] run hello world on multiple server > Message-ID: > < > CAFNNHkwpqdGfZXctL0Uz3hpeL25mZZMtB93qGXjc_+tjnV4csA(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > Sorry to bother you guys on this stupid question. last time I re-install OS > for all blades to keep them the same version. after I mount, set keyless > ssh, the terimnal gives the error below: > > [proxy:0:[email protected]] HYDU_sock_connect > (./utils/sock/sock.c:174): unable to connect from "iocfccd3.aps.anl.gov" > to > "iocfccd1.aps.anl.gov" (No route to host) > [proxy:0:[email protected]] main (./pm/pmiserv/pmip.c:189): unable to > connect to server iocfccd1.aps.anl.gov at port 38242 (check for > firewalls!) > > I can ssh from iocfccd1 to iocfccd3 without password. Should I shut down > all firewalls on each server? I cannot find out where is the problem. Thank > you > > -- > Best Regards, > Sufeng Niu > ECASP lab, ECE department, Illinois Institute of Technology > Tel: 312-731-7219 >

1 0

Re: [mpich-discuss] Problem reproducing an example from the MPI standard
by Jiri Simsa 22 Jun '13

22 Jun '13

Nevermind. I was incorrectly using the MPI_REAL data type. After replacing it with the MPI_DOUBLE data type the program was as expected. On Sat, Jun 22, 2013 at 12:49 PM, Jiri Simsa <jsimsa(a)cs.cmu.edu> wrote: > Hi, > > I tried implementing the Example 3.17 from the MPI 3.0 specification > document using as follows: > > #include <assert.h> > #include <mpi.h> > #include <stdio.h> > > int main(int argc, char *argv[]) { > int myrank, size; > MPI_Status status; > MPI_Init(&argc, &argv ); > MPI_Comm_rank(MPI_COMM_WORLD, &myrank); > MPI_Comm_size(MPI_COMM_WORLD, &size); > assert(size == 3); > if (myrank == 0) { > /* code for process zero */ > int i = 1; > MPI_Send(&i, 1, MPI_INTEGER, 2, 99, MPI_COMM_WORLD); > } > if (myrank == 1) { > /* code for process one */ > double d = 3.14; > MPI_Send(&d, 1, MPI_REAL, 2, 99, MPI_COMM_WORLD); > } > if (myrank == 2) { > /* code for process two */ > for (int i = 0; i < 2; i++) { > MPI_Probe(MPI_ANY_SOURCE, MPI_ANY_TAG, MPI_COMM_WORLD, &status); > printf("Probe matched %lld bytes from source %d.\n", > status.count, status.MPI_SOURCE); > if (status.MPI_SOURCE == 0) { > int i; > MPI_Recv(&i, 1, MPI_INTEGER, 0, 99, MPI_COMM_WORLD, &status); > printf("Received integer '%d' from %d.\n", i, status.MPI_SOURCE); > } else { > double d; > MPI_Recv(&d, 1, MPI_REAL, 1, 99, MPI_COMM_WORLD, &status); > printf("Received real '%f' from %d.\n", d, status.MPI_SOURCE); > } > } > } > MPI_Finalize(); > return 0; > } > > This example compiles without any warning with the MPICH-3.0.4 library. > However, running: > > $ mpiexec -n 3 ./example > > leads to the following output: > > Probe matched 4 bytes from source 1. > Received real '0.000000' from 1. > Probe matched 4 bytes from source 0. > Received integer '1' from 0. > > Could someone please let me know what is the problem with my program? I > failed to see a problem there. Thank you. > > Best, > > --Jiri Simsa >

1 0