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

Segmentation fault (signal 11) and Exit code 139
by Zheng Li 09 Jul '13

09 Jul '13

Dear All, I tried to run the default January 2000 Case (the East Coast Winter Storm of January 24-25, 2000) in WRF v3.5, and failed when running wrf.exe. The error is as follows: [sl@sl0 em_real]$ mpirun -np 4 ./wrf.exe starting wrf task 0 of 4 starting wrf task 1 of 4 starting wrf task 2 of 4 starting wrf task 3 of 4 =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 139 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES =================================================================================== YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11) This typically refers to a problem with your application. Please see the FAQ page for debugging suggestions Does someone have idea of resolving this issue? Thanks in advance. Lee <seraphzl(a)gmail.com>

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an FC-Serial symbol
by Sara Yzdn 09 Jul '13

09 Jul '13

Hi, I have built a code by mpich, but I want to define an FC_SERIAL symbol on top of the makefile. How can I do it correctly? Regards,

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Re: [mpich-discuss] Support for MIC in MPICH 3.0.4
by Maciej.Golebiewski＠csiro.au 08 Jul '13

08 Jul '13

Hi Pavan, Thanks for your reply, although it is not what I hoped to hear. Unfortunately the MPI application I'm trying to run would require too much effort to convert to hybrid OpenMP/MPI to be viable option at this point. I wonder how IntelMPI is working around this limit (I've run it with up to 2 (host) + 2 x 240 (MIC) ranks). Anyway, thanks again and I guess I will have to wait for the updates to MPSS/SCIF. Cheers, Maciej > -----Original Message----- > From: Pavan Balaji [mailto:[email protected]] > Sent: Tuesday, July 09, 2013 12:32 AM > To: discuss(a)mpich.org > Cc: Golebiewski, Maciej (CSIRO IM&T, Docklands) > Subject: Re: [mpich-discuss] Support for MIC in MPICH 3.0.4 > > Hi Maciej, > > Intel is aware of this problem that occurs when a large number of > MIC processes are used. They are looking into it. Right now, the > only workaround we can offer is to use fewer MIC processes and use > threads on the MIC instead. > > -- Pavan > > On 07/08/2013 01:34 AM, Maciej.Golebiewski(a)csiro.au wrote: > > Hi, > > > > I have managed to build MPICH for MIC device and for host system > with support for SCIF and using Intel compilers. I am able to start > MPI processes on MIC device using mpirun from host or mpiexec on > the device itself. > > > > I can also run application with some ranks on the host and some > on the device. > > > > I can't however start more than 4 ranks on any device, if I try > to run my application across more than 1 node (be it host or MIC > cards): > > > > env I_MPI_MIC=enable mpirun -n 1 -host mike.it.csiro.au ./mpptest > -bcast : -n 30 -host mic0 /tmp/mpptest.scif -bcast > > 0: 1: 00000011: 00000170: readv err 0 Fatal error in > MPI_Allreduce: > > Other MPI error, error stack: > > MPI_Allreduce(861)...............: > MPI_Allreduce(sbuf=0x7fff62945a08, > > rbuf=0x7c5de0, count=1, MPI_DOUBLE, MPI_MAX, MPI_COMM_WORLD) > failed > > MPIR_Allreduce_impl(719).........: > > MPIR_Allreduce_intra(201)........: > > allreduce_intra_or_coll_fn(110)..: > > MPIR_Allreduce_intra(362)........: > > MPIC_Sendrecv(213)...............: > > MPIC_Wait(569)...................: > > MPIDI_CH3I_Progress(367).........: > > MPID_nem_mpich_blocking_recv(894): > > state_commrdy_handler(175).......: > > state_commrdy_handler(138).......: > > MPID_nem_scif_recv_handler(115)..: Communication error with rank > 1 > > [...bunch of more error messages follows...] > > > > This problem does not occur of all ranks run on the same node: > > > > env I_MPI_MIC=enable mpirun -n 30 -host mic0 /tmp/mpptest.scif - > bcast > > set default set font variable set curve window y 0.15 0.90 set > order d > > d d x y d title left 'time (us)', bottom 'Size (bytes)', > > top 'Comm Perf for MPI (pkmic-mic0)', > > 'type = blocking' > > > > #p0 p1 dist len ave time (us) rate > > 0 29 29 0 11.448860 0.00 > > 0 29 29 32 12.009144 2.665e+6 > > [...more expected output follows...] > > > > Last November there was a short thread on this list (archive: > http://lists.mpich.org/pipermail/discuss/2012-November/000109.html) > about seemingly similiar problem, but seemed to fizzle out before > any solution was offered. > > > > I wonder whether there was any progress on it, or perhaps someone > else has encountered this problem, too and managed to find a > workaround/solution or at least has an explanation as to what is > happening. > > > > In case someone would like to try and reproduce it, my configure > invocation for MPICH on MIC was: > > > > ./configure CC="icc" CXX=icpc F77="ifort -warn noalignments" > FC="ifort > > -warn noalignments" \ CXXFLAGS=-mmic CFLAGS=-mmic FFLAGS=-mmic > > FCFLAGS=-mmic \ MPICHLIB_CFLAGS="-g" MPICHLIB_CXXFLAGS="-g" > > MPICHLIB_FFLAGS="-g" MPICHLIB_FCFLAGS="-g" \ MPICHLIB_LDFLAGS="- > g" > > LIBS=-lscif LDFLAGS=-L/opt/intel/mic/filesystem/base/lib64 \ > > --with-device=ch3:nemesis:scif,tcp --disable-romio --disable-mpe > > --enable-smpcoll \ --enable-fast=defopt > > --prefix=/apps/mpich-scif/3.0.4/mic --enable-error- > checking=runtime \ > > --enable-timing=runtime --host=i686-linux-gnu \ > > --with-cross=maint/fcrosscompile/cross_values.txt.mike > > > > The settings in cross_values.txt.mike were: > > > > # The Fortran related cross compilation values. > > CROSS_F77_SIZEOF_INTEGER="4" > > CROSS_F77_SIZEOF_REAL="4" > > CROSS_F77_SIZEOF_DOUBLE_PRECISION="8" > > CROSS_F77_TRUE_VALUE="-1" > > CROSS_F77_FALSE_VALUE="0" > > CROSS_F90_ADDRESS_KIND="8" > > CROSS_F90_OFFSET_KIND="8" > > CROSS_F90_INTEGER_KIND="4" > > CROSS_F90_REAL_MODEL=" 6 , 37" > > CROSS_F90_DOUBLE_MODEL=" 15 , 307" > > CROSS_F90_INTEGER_MODEL=" 9" > > CROSS_F90_ALL_INTEGER_MODELS=" 2 , 1, 4 , 2, 9 , 4, 18 , 8," > > CROSS_F90_INTEGER_MODEL_MAP=" { 2 , 1 , 1 }, { 4 , 2 , 2 }, { > 9 , 4 , 4 }, { 18 , 8 , 8 }," > > > > And finally, the configure invocation for MPICH on the host was: > > > > ./configure CC="icc" CXX=icpc F77="ifort -warn noalignments" > FC="ifort > > -warn noalignments" \ MPICHLIB_CFLAGS="-g" MPICHLIB_CXXFLAGS="-g" > > MPICHLIB_FFLAGS="-g" MPICHLIB_FCFLAGS="-g" \ MPICHLIB_LDFLAGS="- > g" > > LIBS=-lscif LDFLAGS=-L/usr/lib64 --with- > device=ch3:nemesis:scif,tcp \ > > --disable-romio --disable-mpe --enable-smpcoll --enable- > fast=defopt \ > > --prefix=/apps/mpich-scif/3.0.4/intel64 > > --enable-error-checking=runtime \ --enable-timing=runtime > > > > Thanks, > > > > Maciej > > > > Maciej Golebiewski > > Applications Support, Advanced Scientific Computing CSIRO IM&T > > > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > -- > Pavan Balaji > http://www.mcs.anl.gov/~balaji

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Re: [mpich-discuss] first exit problems
by Gideon Simpson 08 Jul '13

08 Jul '13

So in a ring termination approach, would it look like: /* On process id n*/ while (!search_complete){ /*Check if a message has been received from process n-1*/ MPI_Iprobe(...,&global_exit_flag,...); /*If no one else finished, continue the algorithm */ if(!global_exit_flag){ /* Step algorithm */ local_exit_flag = exit_test(...); } /*If a message was received to terminate, or an exit is found, alert the neighbors */ if(global_exit_flag || local_exit_flag){ /* If an exit is found somewhere, tell n+1 to stop working */ MPI_ISend(...); /* If an exit has been found, a message has been received from process n-1 */ MPI_Recv(...); /* Loop is only exited on each process after it has sent to n+1 and received from n-1 search_complete = 1; } } /* Sort out any tie breaking down here and reduce as needed*/ Is that an appropriate use of blocked/non-blocked communication? -gideon On Jul 8, 2013, at 12:22 PM, discuss-request(a)mpich.org wrote: > Date: Mon, 8 Jul 2013 12:05:48 -0500 > From: Jeff Hammond <jeff.science(a)gmail.com> > To: discuss(a)mpich.org > Subject: Re: [mpich-discuss] first exit problems > Message-ID: > <CAGKz=uKSbXpNkUU3H9FgmbCOAk_G5roMO-wy9vx1bLukkY62=Q(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Your global exit is going to end up being collective, right? In that > case, you can break ties manually. I don't think you need a > master-worker model either. Just setup a ring and signal termination > to the right neighbor. Everyone will stop after whatever local step > they were in before polling and then you do e.g. a Gather and have the > root sort out which was the true first passage, in the event that more > than one process found a passage during that iteration. > > Jeff > > On Mon, Jul 8, 2013 at 11:02 AM, Gideon Simpson > <gideon.simpson(a)gmail.com> wrote: >> Hi, I was wondering if someone had a good MPI solution to the following first passage problem. Suppose I have N workers, each using a Monte Carlo method to solve a problem. An example would be if I wanted to find the exit distribution in time and space of a stochastic differential equation from some compact set in space. >> >> Assuming that each worker is properly receiving an independent stream of pseudo random numbers, and they are computing asynchronously, when one worker finds a solution, he must notify the others that they can cease working, and the program can continue. I have in mind something like: >> >> while (!local_exit & !global_exit){ >> >> /*Check if a message has been received*/ >> MPI_Iprobe(...,&global_exit,...); >> >> /*If no one else finished, continue the algorithm */ >> if(!global_exit){ >> /* Step algorithm */ >> local_exit = exit_test(...); >> } >> } >> >> if(local_exit){ >> >> /* Alert all other workers */ >> for(...){ >> MPI_Isend(...); >> } >> >> } >> else{ >> >> /* Receive the message that was sent from the other worker */ >> >> MPI_Recv(...); >> } >> >> However, I believe this leads to a race condition because if processor 0 finds and exit, processor 1 might also find one before processor 0 has a chance to do an MPI_Isend() to 1. Assuming that, for the moment, I am not too concerned about tie breaking, I would really like to find a robust solution to this problem, as I have a lot of first exit/first passage type problems that could be solved asynchronously. >> >> Thanks for any suggestions, >> >> -gideon >> >> _______________________________________________ >> 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 on Mac os x
by Reem Alraddadi 08 Jul '13

08 Jul '13

Hi Wesley, Hi Pavan, I will do that. Thanks for all your helps. As I mentioned before, I am still beginner with all this. I will read these links to understand very well how to use MPI_COMM_FREE Thanks again, Reem > Message: 3 > Date: Mon, 8 Jul 2013 12:22:55 -0500 > From: Wesley Bland <wbland(a)mcs.anl.gov> > To: discuss(a)mpich.org > Subject: Re: [mpich-discuss] mpich on Mac os x > Message-ID: <0A10C046-D447-45E0-BD4C-CD6CE7F12D92(a)mcs.anl.gov> > Content-Type: text/plain; charset=us-ascii > > Pavan is probably right that this a problem with the application you're > trying to run. You should probably talk to them. However, if you're trying > to write an MPI problem, you must understand how MPI_COMM_FREE works. > Here's a couple of good links: > > http://www.mcs.anl.gov/research/projects/mpi/www/www3/MPI_Comm_free.html > http://mpi.deino.net/mpi_functions/MPI_Comm_free.html > > On Jul 8, 2013, at 11:56 AM, Jeff Hammond <jeff.science(a)gmail.com> wrote: > > > Do you understand the different between a Fortran procedure/subroutine > > and a variable value? > > > > You cannot set an MPI communicator equal to a subroutine. That makes > > no sense and the compiler is rightfully complaining about it. > > > > Jeff > > > > On Mon, Jul 8, 2013 at 11:32 AM, Reem Alraddadi <raba500(a)york.ac.uk> > wrote: > >> > >> Hi Wesley, > >> > >> How could I do that? as I read in the internet. I have to set: > >> include "mpif.h" > >> Call MPI_COMM_FREE > >> > >> I found where I can set that in FLASH code ( I have attached the file) > So I > >> set: > >> integer, parameter :: FLASH_COMM = MPI_COMM_FREE > >> but I got an error when I compile the code: > >> > >> Included at Driver_abortFlash.F90:34: > >> > >> integer, parameter :: FLASH_COMM = MPI_COMM_FREE > >> 1 > >> Error: Symbol 'flash_comm' at (1) already has basic type of INTEGER > >> make: *** [Driver_abortFlash.o] Error 1 > >> > >> the code used MPI_COMM_WORLD. > >> So is there a way to fix that? > >> > >> Thanks, > >> Reem > >> > >> > >> > >>> Date: Mon, 8 Jul 2013 10:25:38 -0500 > >>> From: Wesley Bland <wbland(a)mcs.anl.gov> > >>> To: discuss(a)mpich.org > >>> Subject: Re: [mpich-discuss] discuss Digest, Vol 9, Issue 13 > >>> Message-ID: <9A8EEBB2-72BB-429B-9368-150983B1C283(a)mcs.anl.gov> > >>> Content-Type: text/plain; charset="iso-8859-1" > >>> > >>> That's the correct way to set that environment variable, but I would > have > >>> to agree with Pavan here. If you're running into the cap on context > id's > >>> (especially with so few processes) it would seem that you're creating > a lot > >>> of communicators that you probably don't need. Are you sure that you're > >>> freeing them correctly after use? > >>> > >>> Wesley > >>> > >>> On Jul 8, 2013, at 10:05 AM, Reem Alraddadi <raba500(a)york.ac.uk> > wrote: > >>> > >>>> Hi Wesley. > >>>> I wrote the following: > >>>> mpirun --np 4 --env MPIR_PARAM_CTXID_EAGER_SIZE 1 ./flash4 > >>>> but the error still the same. Did I do it in the wrong way?? > >>>> > >>>> Thanks, > >>>> Reem > >>>> > >>>> Message: 5 > >>>> Date: Mon, 8 Jul 2013 08:14:48 -0500 > >>>> From: Wesley Bland <wbland(a)mcs.anl.gov> > >>>> To: discuss(a)mpich.org > >>>> Subject: Re: [mpich-discuss] mpich on Mac os x > >>>> Message-ID: <8DC984B2-4E4B-4BFE-806E-203463A7A4E4(a)mcs.anl.gov> > >>>> Content-Type: text/plain; charset=iso-8859-1 > >>>> > >>>> It seems that you're creating more communicators than MPICH can > handle. > >>>> It's possible that you might be able to get around this by setting the > >>>> environment variable MPIR_PARAM_CTXID_EAGER_SIZE to something smaller > than > >>>> its default (which is 2). That frees up a few more communicators, but > there > >>>> is a pathological case where even with fewer communicators than the > max, > >>>> MPICH won't be able to agree on a new communicator id when needed. Try > >>>> changing that environment variable and see if that fixes things. > >>>> > >>>> Wesley > >>>> > >>>> On Jul 8, 2013, at 5:33 AM, Reem Alraddadi <raba500(a)york.ac.uk> > wrote: > >>>> > >>>>> Hi all, > >>>>> I am using mpich-3.0.4 on Mac os x version 10.7.5 to run FLASH code. > >>>>> It works fine in the beginning of the run and then I got the > following > >>>>> error: > >>>>> > >>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: > >>>>> MPI_Comm_create(600).................: > >>>>> MPI_Comm_create(comm=0x84000002, group=0xc8001349, > new_comm=0x7fff606a8614) > >>>>> failed > >>>>> MPI_Comm_create(577).................: > >>>>> MPIR_Comm_create_intra(241)..........: > >>>>> MPIR_Get_contextid(799)..............: > >>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID > >>>>> because of fragmentation (169/2048 free on this process; ignore_id=0) > >>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: > >>>>> MPI_Comm_create(600).................: > >>>>> MPI_Comm_create(comm=0x84000002, group=0xc80012b6, > new_comm=0x7fff670cc614) > >>>>> failed > >>>>> MPI_Comm_create(577).................: > >>>>> MPIR_Comm_create_intra(241)..........: > >>>>> MPIR_Get_contextid(799)..............: > >>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID > >>>>> because of fragmentation (316/2048 free on this process; ignore_id=0) > >>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: > >>>>> MPI_Comm_create(600).................: > >>>>> MPI_Comm_create(comm=0x84000004, group=0xc800000e, > new_comm=0x7fff629d5614) > >>>>> failed > >>>>> MPI_Comm_create(577).................: > >>>>> MPIR_Comm_create_intra(241)..........: > >>>>> MPIR_Get_contextid(799)..............: > >>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID > >>>>> because of fragmentation (2020/2048 free on this process; > ignore_id=0) > >>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: > >>>>> MPI_Comm_create(600).................: > >>>>> MPI_Comm_create(comm=0x84000002, group=0xc8000020, > new_comm=0x7fff639ae614) > >>>>> failed > >>>>> MPI_Comm_create(577).................: > >>>>> MPIR_Comm_create_intra(241)..........: > >>>>> MPIR_Get_contextid(799)..............: > >>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID > >>>>> because of fragmentation (2002/2048 free on this process; ignore_id=0 > >>>>> > >>>>> Is there a way to fix that ? > >>>>> > >>>>> Thanks, > >>>>> Reem > >> > >> > >>> > >>> On Mon, Jul 8, 2013 at 9:17 AM, Pavan Balaji <balaji(a)mcs.anl.gov> > wrote: > >>>> > >>>> Also make sure you are freeing unused communicators. > >>>> > >>>> -- Pavan > >>>> > >>>> On 07/08/2013 08:14 AM, Wesley Bland wrote: > >>>>> > >>>>> It seems that you're creating more communicators than MPICH can > handle. > >>>>> It's possible that you might be able to get around this by setting > the > >>>>> environment variable MPIR_PARAM_CTXID_EAGER_SIZE to something smaller > >>>>> than > >>>>> its default (which is 2). That frees up a few more communicators, but > >>>>> there > >>>>> is a pathological case where even with fewer communicators than the > >>>>> max, > >>>>> MPICH won't be able to agree on a new communicator id when needed. > Try > >>>>> changing that environment variable and see if that fixes things. > >>>>> > >>>>> Wesley > >>>>> > >>>>> On Jul 8, 2013, at 5:33 AM, Reem Alraddadi <raba500(a)york.ac.uk> > wrote: > >>>>> > >>>>>> Hi all, > >>>>>> I am using mpich-3.0.4 on Mac os x version 10.7.5 to run FLASH code. > >>>>>> It > >>>>>> works fine in the beginning of the run and then I got the following > >>>>>> error: > >>>>>> > >>>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: > >>>>>> MPI_Comm_create(600).................: > >>>>>> MPI_Comm_create(comm=0x84000002, > >>>>>> group=0xc8001349, new_comm=0x7fff606a8614) failed > >>>>>> MPI_Comm_create(577).................: > >>>>>> MPIR_Comm_create_intra(241)..........: > >>>>>> MPIR_Get_contextid(799)..............: > >>>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID > >>>>>> because of fragmentation (169/2048 free on this process; > ignore_id=0) > >>>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: > >>>>>> MPI_Comm_create(600).................: > >>>>>> MPI_Comm_create(comm=0x84000002, > >>>>>> group=0xc80012b6, new_comm=0x7fff670cc614) failed > >>>>>> MPI_Comm_create(577).................: > >>>>>> MPIR_Comm_create_intra(241)..........: > >>>>>> MPIR_Get_contextid(799)..............: > >>>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID > >>>>>> because of fragmentation (316/2048 free on this process; > ignore_id=0) > >>>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: > >>>>>> MPI_Comm_create(600).................: > >>>>>> MPI_Comm_create(comm=0x84000004, > >>>>>> group=0xc800000e, new_comm=0x7fff629d5614) failed > >>>>>> MPI_Comm_create(577).................: > >>>>>> MPIR_Comm_create_intra(241)..........: > >>>>>> MPIR_Get_contextid(799)..............: > >>>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID > >>>>>> because of fragmentation (2020/2048 free on this process; > ignore_id=0) > >>>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: > >>>>>> MPI_Comm_create(600).................: > >>>>>> MPI_Comm_create(comm=0x84000002, > >>>>>> group=0xc8000020, new_comm=0x7fff639ae614) failed > >>>>>> MPI_Comm_create(577).................: > >>>>>> MPIR_Comm_create_intra(241)..........: > >>>>>> MPIR_Get_contextid(799)..............: > >>>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID > >>>>>> because of fragmentation (2002/2048 free on this process; > ignore_id=0 > >>>>>> > >>>>>> Is there a way to fix that ? > >>>>>> > >>>>>> Thanks, > >>>>>> Reem > >>>>>> _______________________________________________ > >>>>>> 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 > >>>>> > >>>> > >>>> -- > >>>> Pavan Balaji > >>>> http://www.mcs.anl.gov/~balaji > >>>> _______________________________________________ > >>>> discuss mailing list discuss(a)mpich.org > >>>> To manage subscription options or unsubscribe: > >>>> https://lists.mpich.org/mailman/listinfo/discuss > >>> > >>> > >>> > >>> -- > >>> Jeff Hammond > >>> jeff.science(a)gmail.com > >>> > >>> > >>> ------------------------------ > >>> > >>> Message: 3 > >>> Date: Mon, 8 Jul 2013 16:39:03 +0100 > >>> From: Reem Alraddadi <raba500(a)york.ac.uk> > >>> To: discuss(a)mpich.org > >>> Subject: [mpich-discuss] mpich on Mac os x > >>> Message-ID: > >>> > >>> <CANKsntEJR0b_TA-tbdBO3fOV2O8PkwTG82a718qZPd3FnEBT3w(a)mail.gmail.com> > >>> Content-Type: text/plain; charset="iso-8859-1" > >>> > >>> Hi Pavan, > >>> > >>> Could you explain more what do you mean by that? I am sorry I am still > >>> beginner in MPICH. > >>> > >>> Hi Wesley, > >>> apologize about my first confused reply I have forgotten to change the > >>> subject. However, as I mentioned I wrote the following line: > >>> > >>> mpirun --np 4 --env MPIR_PARAM_CTXID_EAGER_SIZE 1 ./flash4 > >>> > >>> I am wondering if I made any mistake here as the problem is still the > same > >>> > >>> Thanks, > >>> Reem > >>> > >>> > >>> > >>> Message: 1 > >>>> Date: Mon, 08 Jul 2013 09:17:00 -0500 > >>>> From: Pavan Balaji <balaji(a)mcs.anl.gov> > >>>> To: discuss(a)mpich.org > >>>> Subject: Re: [mpich-discuss] mpich on Mac os x > >>>> Message-ID: <51DAC9DC.5000502(a)mcs.anl.gov> > >>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >>>> > >>>> > >>>> Also make sure you are freeing unused communicators. > >>>> > >>>> -- Pavan > >>>> > >>>> On 07/08/2013 08:14 AM, Wesley Bland wrote: > >>>>> It seems that you're creating more communicators than MPICH can > >>>>> handle. > >>>> It's possible that you might be able to get around this by setting the > >>>> environment variable MPIR_PARAM_CTXID_EAGER_SIZE to something smaller > >>>> than > >>>> its default (which is 2). That frees up a few more communicators, but > >>>> there > >>>> is a pathological case where even with fewer communicators than the > max, > >>>> MPICH won't be able to agree on a new communicator id when needed. Try > >>>> changing that environment variable and see if that fixes things. > >>>>> > >>>>> Wesley > >>>>> > >>>>> On Jul 8, 2013, at 5:33 AM, Reem Alraddadi <raba500(a)york.ac.uk> > wrote: > >>>>> > >>>>>> Hi all, > >>>>>> I am using mpich-3.0.4 on Mac os x version 10.7.5 to run FLASH code. > >>>>>> It > >>>> works fine in the beginning of the run and then I got the following > >>>> error: > >>>>>> > >>>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: > >>>>>> MPI_Comm_create(600).................: > >>>>>> MPI_Comm_create(comm=0x84000002, > >>>> group=0xc8001349, new_comm=0x7fff606a8614) failed > >>>>>> MPI_Comm_create(577).................: > >>>>>> MPIR_Comm_create_intra(241)..........: > >>>>>> MPIR_Get_contextid(799)..............: > >>>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID > >>>> because of fragmentation (169/2048 free on this process; ignore_id=0) > >>>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: > >>>>>> MPI_Comm_create(600).................: > >>>>>> MPI_Comm_create(comm=0x84000002, > >>>> group=0xc80012b6, new_comm=0x7fff670cc614) failed > >>>>>> MPI_Comm_create(577).................: > >>>>>> MPIR_Comm_create_intra(241)..........: > >>>>>> MPIR_Get_contextid(799)..............: > >>>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID > >>>> because of fragmentation (316/2048 free on this process; ignore_id=0) > >>>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: > >>>>>> MPI_Comm_create(600).................: > >>>>>> MPI_Comm_create(comm=0x84000004, > >>>> group=0xc800000e, new_comm=0x7fff629d5614) failed > >>>>>> MPI_Comm_create(577).................: > >>>>>> MPIR_Comm_create_intra(241)..........: > >>>>>> MPIR_Get_contextid(799)..............: > >>>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID > >>>> because of fragmentation (2020/2048 free on this process; ignore_id=0) > >>>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: > >>>>>> MPI_Comm_create(600).................: > >>>>>> MPI_Comm_create(comm=0x84000002, > >>>> group=0xc8000020, new_comm=0x7fff639ae614) failed > >>>>>> MPI_Comm_create(577).................: > >>>>>> MPIR_Comm_create_intra(241)..........: > >>>>>> MPIR_Get_contextid(799)..............: > >>>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID > >>>> because of fragmentation (2002/2048 free on this process; ignore_id=0 > >>>>>> > >>>>>> Is there a way to fix that ? > >>>>>> > >>>>>> Thanks, > >>>>>> Reem > >>>>>> _______________________________________________ > >>>>>> 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 > >>>>> > >>>> > >>>> -- > >>>> Pavan Balaji > >>>> http://www.mcs.anl.gov/~balaji > >>>> > >>>

1 0

Re: [mpich-discuss] "undefined references"
by Wesley Bland 08 Jul '13

08 Jul '13

We're not going to be able to help you debug other packages here. You're going to need to talk to the Siesta people about this. On Jul 8, 2013, at 12:15 PM, Hana Milani <hana.milani(a)yahoo.com> wrote: > I have also tried to install serial Siesta and "make" gen basis. Here is the error I get: > > alloc.o basis_types.o precision.o recipes.o parallel.o parsing.o xcmod.o basis_io.o chemical.o atm_transfer.o atm_types.o atmparams.o old_atmfuncs.o radial.o io.o paste.o flib_spline.o bessph.o m_filter.o basis_specs.o atom.o memoryinfo.o memory.o periodic_table.o pseudopotential.o pxf.o dot.o xc.o atom_options.o arw.o sys.o timer.o xml.o m_walltime.o gen-basis.o nag.o libfdf.a dc_lapack.a liblapack.a libblas.a > f95: error: dc_lapack.a: No such file or directory > f95: error: liblapack.a: No such file or directory > f95: error: libblas.a: No such file or directory > make: *** [gen-basis] Error 1 > > why should it ask for liblapack when I have installed siesta in parallel with absolutely n change in arch.make !!!! > > > > From: Jeff Hammond <jeff.science(a)gmail.com> > To: Hana Milani <hana.milani(a)yahoo.com>; discuss(a)mpich.org > Sent: Monday, July 8, 2013 8:56 PM > Subject: Re: [mpich-discuss] "undefined references" > > I looked through the code and suspect Siesta is at fault but since > they rolled their own MPI F90 wrappers and I know very little about > F90, I cannot debug it. > > You will see that there are no wrappers for send, recv, bcast or > reduce (the functions for which you get errors) in ./Src/MPI/mpi.F. > There are references to these in ./Src/MPI/mpi__*.f90 but I don't > understand what's going on very well. It also appears that these > files are from a prototype implementation of the F90 module for MPI > 1.1 written in 1996. I don't know if that was before the MPI standard > defined F90 bindings, but it surely does now and applications should > use those instead. > > The other thing you can do is turn off MPI in the utility code since > it might not be necessary there. > > Jeff > > On Mon, Jul 8, 2013 at 11:09 AM, Hana Milani <hana.milani(a)yahoo.com> wrote: > > yes, apologies > > > > ________________________________ > > From: Hana Milani <hana.milani(a)yahoo.com> > > To: Pavan Balaji <balaji(a)mcs.anl.gov> > > Sent: Monday, July 8, 2013 7:53 PM > > > > Subject: Re: [mpich-discuss] "undefined references" > > > > yes Pavan, But it's a long time I have not received any response > > > > > > ________________________________ > > From: Pavan Balaji <balaji(a)mcs.anl.gov> > > To: Hana Milani <hana.milani(a)yahoo.com>; discuss(a)mpich.org > > Sent: Monday, July 8, 2013 7:03 PM > > > > Subject: Re: [mpich-discuss] "undefined references" > > > > > > This doesn't look like an MPI error. Did you contact the authors of > > whatever package you are trying to compile? > > > > -- Pavan > > > > On 07/08/2013 08:25 AM, Hana Milani wrote: > >> Hello, > >> > >> I have compiled a code (siesta) by mpich2, blacs, lapack, blas and > >> scalapack. It works fine under grid computation. But when I want to > >> "make" a utility, I receive the following errors: > >> > >> [Home@localhost Gen-basis]$ make > >> /usr/local/bin/mpif90 -o gen-basis \ > >> alloc.o basis_types.o precision.o recipes.o parallel.o > >> parsing.o xcmod.o basis_io.o chemical.o atm_transfer.o atm_types.o > >> atmparams.o old_atmfuncs.o radial.o io.o paste.o flib_spline.o > >> bessph.o m_filter.o basis_specs.o atom.o memoryinfo.o memory.o > >> periodic_table.o pseudopotential.o pxf.o dot.o xc.o atom_options.o > >> arw.o sys.o timer.o xml.o m_walltime.o gen-basis.o nag.o libfdf.a > >> /home/Home/Packages/scalapack-2.0.2/libscalapack.a > >> /home/Home/Packages/BLACS/LIB/blacsCinit_MPI-LINUX-0.a > >> /home/Home/Packages/BLACS/LIB/blacsF77init_MPI-LINUX-0.a > >> /home/Home/Packages/BLACS/LIB/blacs_MPI-LINUX-0.a > >> /home/Home/Packages/lapack-3.4.2/liblapack.a > >> /home/Home/Packages/BLAS/blas_LINUX.a > >> alloc.o: In function `print_report': > >> > >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/alloc.F90:1705: > >> undefined reference to `__mpi__r8_s_MOD_mpi_reduce_t' > >> > >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/alloc.F90:1707: > >> undefined reference to `__mpi__r8_v_MOD_mpi_reduce_t' > >> > >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/alloc.F90:1711: > >> undefined reference to `__mpi__integer_s_MOD_mpi_bcast_t' > >> > >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/alloc.F90:1723: > >> undefined reference to `__mpi__r8_s_MOD_mpi_recv_t' > >> > >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/alloc.F90:1718: > >> undefined reference to `__mpi__r8_s_MOD_mpi_send_t' > >> alloc.o: In function `__alloc_MOD_alloc_report': > >> > >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/alloc.F90:318: > >> undefined reference to `__mpi__integer_s_MOD_mpi_bcast_t' > >> > >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/alloc.F90:319: > >> undefined reference to `__mpi__integer_s_MOD_mpi_bcast_t' > >> > >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/alloc.F90:320: > >> undefined reference to `__mpi__character_s_MOD_mpi_bcast_t' > >> xcmod.o: In function `__xcmod_MOD_setxc': > >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/xcmod.F:136: > >> undefined > >> reference to `__mpi__integer_s_MOD_mpi_bcast_t' > >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/xcmod.F:138: > >> undefined > >> reference to `__mpi__character_v_MOD_mpi_bcast_t' > >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/xcmod.F:140: > >> undefined > >> reference to `__mpi__character_v_MOD_mpi_bcast_t' > >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/xcmod.F:142: > >> undefined > >> reference to `__mpi__r8_v_MOD_mpi_bcast_t' > >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/xcmod.F:144: > >> undefined > >> reference to `__mpi__r8_v_MOD_mpi_bcast_t' > >> memory.o: In function `printmemory_': > >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/memory.F:144: > >> undefined reference to `__mpi__integer_s_MOD_mpi_allreduce_t' > >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/memory.F:167: > >> undefined reference to `__mpi__integer_sv_MOD_mpi_gather_t' > >> timer.o: In function `timer1_': > >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/timer.F:117: > >> undefined > >> reference to `__mpi__r8_s_MOD_mpi_allreduce_t' > >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/timer.F:164: > >> undefined > >> reference to `__mpi__r8_v_MOD_mpi_reduce_t' > >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/timer.F:139: > >> undefined > >> reference to `__mpi__r8_v_MOD_mpi_reduce_t' > >> collect2: error: ld returned 1 exit status > >> make: *** [gen-basis] Error 1 > >> > >> I will be really grateful if you kindly help me to solve this problem. > >> > >> > >> _______________________________________________ > >> discuss mailing list discuss(a)mpich.org > >> To manage subscription options or unsubscribe: > >> https://lists.mpich.org/mailman/listinfo/discuss > >> > > > > -- > > Pavan Balaji > > http://www.mcs.anl.gov/~balaji > > > > > > > > > > > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > -- > Jeff Hammond > jeff.science(a)gmail.com > > > _______________________________________________ > 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] mpich on Mac os x
by Wesley Bland 08 Jul '13

08 Jul '13

Pavan is probably right that this a problem with the application you're trying to run. You should probably talk to them. However, if you're trying to write an MPI problem, you must understand how MPI_COMM_FREE works. Here's a couple of good links: http://www.mcs.anl.gov/research/projects/mpi/www/www3/MPI_Comm_free.html http://mpi.deino.net/mpi_functions/MPI_Comm_free.html On Jul 8, 2013, at 11:56 AM, Jeff Hammond <jeff.science(a)gmail.com> wrote: > Do you understand the different between a Fortran procedure/subroutine > and a variable value? > > You cannot set an MPI communicator equal to a subroutine. That makes > no sense and the compiler is rightfully complaining about it. > > Jeff > > On Mon, Jul 8, 2013 at 11:32 AM, Reem Alraddadi <raba500(a)york.ac.uk> wrote: >> >> Hi Wesley, >> >> How could I do that? as I read in the internet. I have to set: >> include "mpif.h" >> Call MPI_COMM_FREE >> >> I found where I can set that in FLASH code ( I have attached the file) So I >> set: >> integer, parameter :: FLASH_COMM = MPI_COMM_FREE >> but I got an error when I compile the code: >> >> Included at Driver_abortFlash.F90:34: >> >> integer, parameter :: FLASH_COMM = MPI_COMM_FREE >> 1 >> Error: Symbol 'flash_comm' at (1) already has basic type of INTEGER >> make: *** [Driver_abortFlash.o] Error 1 >> >> the code used MPI_COMM_WORLD. >> So is there a way to fix that? >> >> Thanks, >> Reem >> >> >> >>> Date: Mon, 8 Jul 2013 10:25:38 -0500 >>> From: Wesley Bland <wbland(a)mcs.anl.gov> >>> To: discuss(a)mpich.org >>> Subject: Re: [mpich-discuss] discuss Digest, Vol 9, Issue 13 >>> Message-ID: <9A8EEBB2-72BB-429B-9368-150983B1C283(a)mcs.anl.gov> >>> Content-Type: text/plain; charset="iso-8859-1" >>> >>> That's the correct way to set that environment variable, but I would have >>> to agree with Pavan here. If you're running into the cap on context id's >>> (especially with so few processes) it would seem that you're creating a lot >>> of communicators that you probably don't need. Are you sure that you're >>> freeing them correctly after use? >>> >>> Wesley >>> >>> On Jul 8, 2013, at 10:05 AM, Reem Alraddadi <raba500(a)york.ac.uk> wrote: >>> >>>> Hi Wesley. >>>> I wrote the following: >>>> mpirun --np 4 --env MPIR_PARAM_CTXID_EAGER_SIZE 1 ./flash4 >>>> but the error still the same. Did I do it in the wrong way?? >>>> >>>> Thanks, >>>> Reem >>>> >>>> Message: 5 >>>> Date: Mon, 8 Jul 2013 08:14:48 -0500 >>>> From: Wesley Bland <wbland(a)mcs.anl.gov> >>>> To: discuss(a)mpich.org >>>> Subject: Re: [mpich-discuss] mpich on Mac os x >>>> Message-ID: <8DC984B2-4E4B-4BFE-806E-203463A7A4E4(a)mcs.anl.gov> >>>> Content-Type: text/plain; charset=iso-8859-1 >>>> >>>> It seems that you're creating more communicators than MPICH can handle. >>>> It's possible that you might be able to get around this by setting the >>>> environment variable MPIR_PARAM_CTXID_EAGER_SIZE to something smaller than >>>> its default (which is 2). That frees up a few more communicators, but there >>>> is a pathological case where even with fewer communicators than the max, >>>> MPICH won't be able to agree on a new communicator id when needed. Try >>>> changing that environment variable and see if that fixes things. >>>> >>>> Wesley >>>> >>>> On Jul 8, 2013, at 5:33 AM, Reem Alraddadi <raba500(a)york.ac.uk> wrote: >>>> >>>>> Hi all, >>>>> I am using mpich-3.0.4 on Mac os x version 10.7.5 to run FLASH code. >>>>> It works fine in the beginning of the run and then I got the following >>>>> error: >>>>> >>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: >>>>> MPI_Comm_create(600).................: >>>>> MPI_Comm_create(comm=0x84000002, group=0xc8001349, new_comm=0x7fff606a8614) >>>>> failed >>>>> MPI_Comm_create(577).................: >>>>> MPIR_Comm_create_intra(241)..........: >>>>> MPIR_Get_contextid(799)..............: >>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >>>>> because of fragmentation (169/2048 free on this process; ignore_id=0) >>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: >>>>> MPI_Comm_create(600).................: >>>>> MPI_Comm_create(comm=0x84000002, group=0xc80012b6, new_comm=0x7fff670cc614) >>>>> failed >>>>> MPI_Comm_create(577).................: >>>>> MPIR_Comm_create_intra(241)..........: >>>>> MPIR_Get_contextid(799)..............: >>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >>>>> because of fragmentation (316/2048 free on this process; ignore_id=0) >>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: >>>>> MPI_Comm_create(600).................: >>>>> MPI_Comm_create(comm=0x84000004, group=0xc800000e, new_comm=0x7fff629d5614) >>>>> failed >>>>> MPI_Comm_create(577).................: >>>>> MPIR_Comm_create_intra(241)..........: >>>>> MPIR_Get_contextid(799)..............: >>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >>>>> because of fragmentation (2020/2048 free on this process; ignore_id=0) >>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: >>>>> MPI_Comm_create(600).................: >>>>> MPI_Comm_create(comm=0x84000002, group=0xc8000020, new_comm=0x7fff639ae614) >>>>> failed >>>>> MPI_Comm_create(577).................: >>>>> MPIR_Comm_create_intra(241)..........: >>>>> MPIR_Get_contextid(799)..............: >>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >>>>> because of fragmentation (2002/2048 free on this process; ignore_id=0 >>>>> >>>>> Is there a way to fix that ? >>>>> >>>>> Thanks, >>>>> Reem >> >> >>> >>> On Mon, Jul 8, 2013 at 9:17 AM, Pavan Balaji <balaji(a)mcs.anl.gov> wrote: >>>> >>>> Also make sure you are freeing unused communicators. >>>> >>>> -- Pavan >>>> >>>> On 07/08/2013 08:14 AM, Wesley Bland wrote: >>>>> >>>>> It seems that you're creating more communicators than MPICH can handle. >>>>> It's possible that you might be able to get around this by setting the >>>>> environment variable MPIR_PARAM_CTXID_EAGER_SIZE to something smaller >>>>> than >>>>> its default (which is 2). That frees up a few more communicators, but >>>>> there >>>>> is a pathological case where even with fewer communicators than the >>>>> max, >>>>> MPICH won't be able to agree on a new communicator id when needed. Try >>>>> changing that environment variable and see if that fixes things. >>>>> >>>>> Wesley >>>>> >>>>> On Jul 8, 2013, at 5:33 AM, Reem Alraddadi <raba500(a)york.ac.uk> wrote: >>>>> >>>>>> Hi all, >>>>>> I am using mpich-3.0.4 on Mac os x version 10.7.5 to run FLASH code. >>>>>> It >>>>>> works fine in the beginning of the run and then I got the following >>>>>> error: >>>>>> >>>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: >>>>>> MPI_Comm_create(600).................: >>>>>> MPI_Comm_create(comm=0x84000002, >>>>>> group=0xc8001349, new_comm=0x7fff606a8614) failed >>>>>> MPI_Comm_create(577).................: >>>>>> MPIR_Comm_create_intra(241)..........: >>>>>> MPIR_Get_contextid(799)..............: >>>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >>>>>> because of fragmentation (169/2048 free on this process; ignore_id=0) >>>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: >>>>>> MPI_Comm_create(600).................: >>>>>> MPI_Comm_create(comm=0x84000002, >>>>>> group=0xc80012b6, new_comm=0x7fff670cc614) failed >>>>>> MPI_Comm_create(577).................: >>>>>> MPIR_Comm_create_intra(241)..........: >>>>>> MPIR_Get_contextid(799)..............: >>>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >>>>>> because of fragmentation (316/2048 free on this process; ignore_id=0) >>>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: >>>>>> MPI_Comm_create(600).................: >>>>>> MPI_Comm_create(comm=0x84000004, >>>>>> group=0xc800000e, new_comm=0x7fff629d5614) failed >>>>>> MPI_Comm_create(577).................: >>>>>> MPIR_Comm_create_intra(241)..........: >>>>>> MPIR_Get_contextid(799)..............: >>>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >>>>>> because of fragmentation (2020/2048 free on this process; ignore_id=0) >>>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: >>>>>> MPI_Comm_create(600).................: >>>>>> MPI_Comm_create(comm=0x84000002, >>>>>> group=0xc8000020, new_comm=0x7fff639ae614) failed >>>>>> MPI_Comm_create(577).................: >>>>>> MPIR_Comm_create_intra(241)..........: >>>>>> MPIR_Get_contextid(799)..............: >>>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >>>>>> because of fragmentation (2002/2048 free on this process; ignore_id=0 >>>>>> >>>>>> Is there a way to fix that ? >>>>>> >>>>>> Thanks, >>>>>> Reem >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>> >>>> -- >>>> Pavan Balaji >>>> http://www.mcs.anl.gov/~balaji >>>> _______________________________________________ >>>> discuss mailing list discuss(a)mpich.org >>>> To manage subscription options or unsubscribe: >>>> https://lists.mpich.org/mailman/listinfo/discuss >>> >>> >>> >>> -- >>> Jeff Hammond >>> jeff.science(a)gmail.com >>> >>> >>> ------------------------------ >>> >>> Message: 3 >>> Date: Mon, 8 Jul 2013 16:39:03 +0100 >>> From: Reem Alraddadi <raba500(a)york.ac.uk> >>> To: discuss(a)mpich.org >>> Subject: [mpich-discuss] mpich on Mac os x >>> Message-ID: >>> >>> <CANKsntEJR0b_TA-tbdBO3fOV2O8PkwTG82a718qZPd3FnEBT3w(a)mail.gmail.com> >>> Content-Type: text/plain; charset="iso-8859-1" >>> >>> Hi Pavan, >>> >>> Could you explain more what do you mean by that? I am sorry I am still >>> beginner in MPICH. >>> >>> Hi Wesley, >>> apologize about my first confused reply I have forgotten to change the >>> subject. However, as I mentioned I wrote the following line: >>> >>> mpirun --np 4 --env MPIR_PARAM_CTXID_EAGER_SIZE 1 ./flash4 >>> >>> I am wondering if I made any mistake here as the problem is still the same >>> >>> Thanks, >>> Reem >>> >>> >>> >>> Message: 1 >>>> Date: Mon, 08 Jul 2013 09:17:00 -0500 >>>> From: Pavan Balaji <balaji(a)mcs.anl.gov> >>>> To: discuss(a)mpich.org >>>> Subject: Re: [mpich-discuss] mpich on Mac os x >>>> Message-ID: <51DAC9DC.5000502(a)mcs.anl.gov> >>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>>> >>>> >>>> Also make sure you are freeing unused communicators. >>>> >>>> -- Pavan >>>> >>>> On 07/08/2013 08:14 AM, Wesley Bland wrote: >>>>> It seems that you're creating more communicators than MPICH can >>>>> handle. >>>> It's possible that you might be able to get around this by setting the >>>> environment variable MPIR_PARAM_CTXID_EAGER_SIZE to something smaller >>>> than >>>> its default (which is 2). That frees up a few more communicators, but >>>> there >>>> is a pathological case where even with fewer communicators than the max, >>>> MPICH won't be able to agree on a new communicator id when needed. Try >>>> changing that environment variable and see if that fixes things. >>>>> >>>>> Wesley >>>>> >>>>> On Jul 8, 2013, at 5:33 AM, Reem Alraddadi <raba500(a)york.ac.uk> wrote: >>>>> >>>>>> Hi all, >>>>>> I am using mpich-3.0.4 on Mac os x version 10.7.5 to run FLASH code. >>>>>> It >>>> works fine in the beginning of the run and then I got the following >>>> error: >>>>>> >>>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: >>>>>> MPI_Comm_create(600).................: >>>>>> MPI_Comm_create(comm=0x84000002, >>>> group=0xc8001349, new_comm=0x7fff606a8614) failed >>>>>> MPI_Comm_create(577).................: >>>>>> MPIR_Comm_create_intra(241)..........: >>>>>> MPIR_Get_contextid(799)..............: >>>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >>>> because of fragmentation (169/2048 free on this process; ignore_id=0) >>>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: >>>>>> MPI_Comm_create(600).................: >>>>>> MPI_Comm_create(comm=0x84000002, >>>> group=0xc80012b6, new_comm=0x7fff670cc614) failed >>>>>> MPI_Comm_create(577).................: >>>>>> MPIR_Comm_create_intra(241)..........: >>>>>> MPIR_Get_contextid(799)..............: >>>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >>>> because of fragmentation (316/2048 free on this process; ignore_id=0) >>>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: >>>>>> MPI_Comm_create(600).................: >>>>>> MPI_Comm_create(comm=0x84000004, >>>> group=0xc800000e, new_comm=0x7fff629d5614) failed >>>>>> MPI_Comm_create(577).................: >>>>>> MPIR_Comm_create_intra(241)..........: >>>>>> MPIR_Get_contextid(799)..............: >>>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >>>> because of fragmentation (2020/2048 free on this process; ignore_id=0) >>>>>> Fatal error in MPI_Comm_create: Other MPI error, error stack: >>>>>> MPI_Comm_create(600).................: >>>>>> MPI_Comm_create(comm=0x84000002, >>>> group=0xc8000020, new_comm=0x7fff639ae614) failed >>>>>> MPI_Comm_create(577).................: >>>>>> MPIR_Comm_create_intra(241)..........: >>>>>> MPIR_Get_contextid(799)..............: >>>>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >>>> because of fragmentation (2002/2048 free on this process; ignore_id=0 >>>>>> >>>>>> Is there a way to fix that ? >>>>>> >>>>>> Thanks, >>>>>> Reem >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>> >>>> -- >>>> Pavan Balaji >>>> http://www.mcs.anl.gov/~balaji >>>> >>>

1 0

Re: [mpich-discuss] "undefined references"
by Hana Milani 08 Jul '13

08 Jul '13

I have also tried to install serial Siesta and "make" gen basis. Here is the error I get: alloc.o basis_types.o precision.o recipes.o parallel.o parsing.o xcmod.o basis_io.o chemical.o atm_transfer.o atm_types.o atmparams.o old_atmfuncs.o radial.o io.o paste.o flib_spline.o bessph.o m_filter.o basis_specs.o atom.o memoryinfo.o memory.o periodic_table.o pseudopotential.o pxf.o dot.o xc.o atom_options.o arw.o sys.o timer.o xml.o m_walltime.o gen-basis.o nag.o libfdf.a dc_lapack.a liblapack.a libblas.a f95: error: dc_lapack.a: No such file or directory f95: error: liblapack.a: No such file or directory f95: error: libblas.a: No such file or directory make: *** [gen-basis] Error 1 why should it ask for liblapack when I have installed siesta in parallel with absolutely n change in arch.make !!!! ________________________________ From: Jeff Hammond <jeff.science(a)gmail.com> To: Hana Milani <hana.milani(a)yahoo.com>; discuss(a)mpich.org Sent: Monday, July 8, 2013 8:56 PM Subject: Re: [mpich-discuss] "undefined references" I looked through the code and suspect Siesta is at fault but since they rolled their own MPI F90 wrappers and I know very little about F90, I cannot debug it. You will see that there are no wrappers for send, recv, bcast or reduce (the functions for which you get errors) in ./Src/MPI/mpi.F. There are references to these in ./Src/MPI/mpi__*.f90 but I don't understand what's going on very well. It also appears that these files are from a prototype implementation of the F90 module for MPI 1.1 written in 1996. I don't know if that was before the MPI standard defined F90 bindings, but it surely does now and applications should use those instead. The other thing you can do is turn off MPI in the utility code since it might not be necessary there. Jeff On Mon, Jul 8, 2013 at 11:09 AM, Hana Milani <hana.milani(a)yahoo.com> wrote: > yes, apologies > > ________________________________ > From: Hana Milani <hana.milani(a)yahoo.com> > To: Pavan Balaji <balaji(a)mcs.anl.gov> > Sent: Monday, July 8, 2013 7:53 PM > > Subject: Re: [mpich-discuss] "undefined references" > > yes Pavan, But it's a long time I have not received any response > > > ________________________________ > From: Pavan Balaji <balaji(a)mcs.anl.gov> > To: Hana Milani <hana.milani(a)yahoo.com>; discuss(a)mpich.org > Sent: Monday, July 8, 2013 7:03 PM > > Subject: Re: [mpich-discuss] "undefined references" > > > This doesn't look like an MPI error. Did you contact the authors of > whatever package you are trying to compile? > > -- Pavan > > On 07/08/2013 08:25 AM, Hana Milani wrote: >> Hello, >> >> I have compiled a code (siesta) by mpich2, blacs, lapack, blas and >> scalapack. It works fine under grid computation. But when I want to >> "make" a utility, I receive the following errors: >> >> [Home@localhost Gen-basis]$ make >> /usr/local/bin/mpif90 -o gen-basis \ >> alloc.o basis_types.o precision.o recipes.o parallel.o >> parsing.o xcmod.o basis_io.o chemical.o atm_transfer.o atm_types.o >> atmparams.o old_atmfuncs.o radial.o io.o paste.o flib_spline.o >> bessph.o m_filter.o basis_specs.o atom.o memoryinfo.o memory.o >> periodic_table.o pseudopotential.o pxf.o dot.o xc.o atom_options.o >> arw.o sys.o timer.o xml.o m_walltime.o gen-basis.o nag.o libfdf.a >> /home/Home/Packages/scalapack-2.0.2/libscalapack.a >> /home/Home/Packages/BLACS/LIB/blacsCinit_MPI-LINUX-0.a >> /home/Home/Packages/BLACS/LIB/blacsF77init_MPI-LINUX-0.a >> /home/Home/Packages/BLACS/LIB/blacs_MPI-LINUX-0.a >> /home/Home/Packages/lapack-3.4.2/liblapack.a >> /home/Home/Packages/BLAS/blas_LINUX.a >> alloc.o: In function `print_report': >> >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/alloc.F90:1705: >> undefined reference to `__mpi__r8_s_MOD_mpi_reduce_t' >> >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/alloc.F90:1707: >> undefined reference to `__mpi__r8_v_MOD_mpi_reduce_t' >> >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/alloc.F90:1711: >> undefined reference to `__mpi__integer_s_MOD_mpi_bcast_t' >> >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/alloc.F90:1723: >> undefined reference to `__mpi__r8_s_MOD_mpi_recv_t' >> >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/alloc.F90:1718: >> undefined reference to `__mpi__r8_s_MOD_mpi_send_t' >> alloc.o: In function `__alloc_MOD_alloc_report': >> >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/alloc.F90:318: >> undefined reference to `__mpi__integer_s_MOD_mpi_bcast_t' >> >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/alloc.F90:319: >> undefined reference to `__mpi__integer_s_MOD_mpi_bcast_t' >> >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/alloc.F90:320: >> undefined reference to `__mpi__character_s_MOD_mpi_bcast_t' >> xcmod.o: In function `__xcmod_MOD_setxc': >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/xcmod.F:136: >> undefined >> reference to `__mpi__integer_s_MOD_mpi_bcast_t' >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/xcmod.F:138: >> undefined >> reference to `__mpi__character_v_MOD_mpi_bcast_t' >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/xcmod.F:140: >> undefined >> reference to `__mpi__character_v_MOD_mpi_bcast_t' >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/xcmod.F:142: >> undefined >> reference to `__mpi__r8_v_MOD_mpi_bcast_t' >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/xcmod.F:144: >> undefined >> reference to `__mpi__r8_v_MOD_mpi_bcast_t' >> memory.o: In function `printmemory_': >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/memory.F:144: >> undefined reference to `__mpi__integer_s_MOD_mpi_allreduce_t' >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/memory.F:167: >> undefined reference to `__mpi__integer_sv_MOD_mpi_gather_t' >> timer.o: In function `timer1_': >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/timer.F:117: >> undefined >> reference to `__mpi__r8_s_MOD_mpi_allreduce_t' >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/timer.F:164: >> undefined >> reference to `__mpi__r8_v_MOD_mpi_reduce_t' >> /home/Home/Packages/siesta-TEST-3.2/Util/Gen-basis/../../Src/timer.F:139: >> undefined >> reference to `__mpi__r8_v_MOD_mpi_reduce_t' >> collect2: error: ld returned 1 exit status >> make: *** [gen-basis] Error 1 >> >> I will be really grateful if you kindly help me to solve this problem. >> >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> > > -- > Pavan Balaji > http://www.mcs.anl.gov/~balaji > > > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- Jeff Hammond jeff.science(a)gmail.com

1 0

Re: [mpich-discuss] first exit problems
by Jeff Hammond 08 Jul '13

08 Jul '13

Your global exit is going to end up being collective, right? In that case, you can break ties manually. I don't think you need a master-worker model either. Just setup a ring and signal termination to the right neighbor. Everyone will stop after whatever local step they were in before polling and then you do e.g. a Gather and have the root sort out which was the true first passage, in the event that more than one process found a passage during that iteration. Jeff On Mon, Jul 8, 2013 at 11:02 AM, Gideon Simpson <gideon.simpson(a)gmail.com> wrote: > Hi, I was wondering if someone had a good MPI solution to the following first passage problem. Suppose I have N workers, each using a Monte Carlo method to solve a problem. An example would be if I wanted to find the exit distribution in time and space of a stochastic differential equation from some compact set in space. > > Assuming that each worker is properly receiving an independent stream of pseudo random numbers, and they are computing asynchronously, when one worker finds a solution, he must notify the others that they can cease working, and the program can continue. I have in mind something like: > > while (!local_exit & !global_exit){ > > /*Check if a message has been received*/ > MPI_Iprobe(...,&global_exit,...); > > /*If no one else finished, continue the algorithm */ > if(!global_exit){ > /* Step algorithm */ > local_exit = exit_test(...); > } > } > > if(local_exit){ > > /* Alert all other workers */ > for(...){ > MPI_Isend(...); > } > > } > else{ > > /* Receive the message that was sent from the other worker */ > > MPI_Recv(...); > } > > However, I believe this leads to a race condition because if processor 0 finds and exit, processor 1 might also find one before processor 0 has a chance to do an MPI_Isend() to 1. Assuming that, for the moment, I am not too concerned about tie breaking, I would really like to find a robust solution to this problem, as I have a lot of first exit/first passage type problems that could be solved asynchronously. > > Thanks for any suggestions, > > -gideon > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- Jeff Hammond jeff.science(a)gmail.com

1 0

Re: [mpich-discuss] mpich on Mac os x
by Jeff Hammond 08 Jul '13

08 Jul '13

Do you understand the different between a Fortran procedure/subroutine and a variable value? You cannot set an MPI communicator equal to a subroutine. That makes no sense and the compiler is rightfully complaining about it. Jeff On Mon, Jul 8, 2013 at 11:32 AM, Reem Alraddadi <raba500(a)york.ac.uk> wrote: > > Hi Wesley, > > How could I do that? as I read in the internet. I have to set: > include "mpif.h" > Call MPI_COMM_FREE > > I found where I can set that in FLASH code ( I have attached the file) So I > set: > integer, parameter :: FLASH_COMM = MPI_COMM_FREE > but I got an error when I compile the code: > > Included at Driver_abortFlash.F90:34: > > integer, parameter :: FLASH_COMM = MPI_COMM_FREE > 1 > Error: Symbol 'flash_comm' at (1) already has basic type of INTEGER > make: *** [Driver_abortFlash.o] Error 1 > > the code used MPI_COMM_WORLD. > So is there a way to fix that? > > Thanks, > Reem > > > >> Date: Mon, 8 Jul 2013 10:25:38 -0500 >> From: Wesley Bland <wbland(a)mcs.anl.gov> >> To: discuss(a)mpich.org >> Subject: Re: [mpich-discuss] discuss Digest, Vol 9, Issue 13 >> Message-ID: <9A8EEBB2-72BB-429B-9368-150983B1C283(a)mcs.anl.gov> >> Content-Type: text/plain; charset="iso-8859-1" >> >> That's the correct way to set that environment variable, but I would have >> to agree with Pavan here. If you're running into the cap on context id's >> (especially with so few processes) it would seem that you're creating a lot >> of communicators that you probably don't need. Are you sure that you're >> freeing them correctly after use? >> >> Wesley >> >> On Jul 8, 2013, at 10:05 AM, Reem Alraddadi <raba500(a)york.ac.uk> wrote: >> >> > Hi Wesley. >> > I wrote the following: >> > mpirun --np 4 --env MPIR_PARAM_CTXID_EAGER_SIZE 1 ./flash4 >> > but the error still the same. Did I do it in the wrong way?? >> > >> > Thanks, >> > Reem >> > >> > Message: 5 >> > Date: Mon, 8 Jul 2013 08:14:48 -0500 >> > From: Wesley Bland <wbland(a)mcs.anl.gov> >> > To: discuss(a)mpich.org >> > Subject: Re: [mpich-discuss] mpich on Mac os x >> > Message-ID: <8DC984B2-4E4B-4BFE-806E-203463A7A4E4(a)mcs.anl.gov> >> > Content-Type: text/plain; charset=iso-8859-1 >> > >> > It seems that you're creating more communicators than MPICH can handle. >> > It's possible that you might be able to get around this by setting the >> > environment variable MPIR_PARAM_CTXID_EAGER_SIZE to something smaller than >> > its default (which is 2). That frees up a few more communicators, but there >> > is a pathological case where even with fewer communicators than the max, >> > MPICH won't be able to agree on a new communicator id when needed. Try >> > changing that environment variable and see if that fixes things. >> > >> > Wesley >> > >> > On Jul 8, 2013, at 5:33 AM, Reem Alraddadi <raba500(a)york.ac.uk> wrote: >> > >> > > Hi all, >> > > I am using mpich-3.0.4 on Mac os x version 10.7.5 to run FLASH code. >> > > It works fine in the beginning of the run and then I got the following >> > > error: >> > > >> > > Fatal error in MPI_Comm_create: Other MPI error, error stack: >> > > MPI_Comm_create(600).................: >> > > MPI_Comm_create(comm=0x84000002, group=0xc8001349, new_comm=0x7fff606a8614) >> > > failed >> > > MPI_Comm_create(577).................: >> > > MPIR_Comm_create_intra(241)..........: >> > > MPIR_Get_contextid(799)..............: >> > > MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >> > > because of fragmentation (169/2048 free on this process; ignore_id=0) >> > > Fatal error in MPI_Comm_create: Other MPI error, error stack: >> > > MPI_Comm_create(600).................: >> > > MPI_Comm_create(comm=0x84000002, group=0xc80012b6, new_comm=0x7fff670cc614) >> > > failed >> > > MPI_Comm_create(577).................: >> > > MPIR_Comm_create_intra(241)..........: >> > > MPIR_Get_contextid(799)..............: >> > > MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >> > > because of fragmentation (316/2048 free on this process; ignore_id=0) >> > > Fatal error in MPI_Comm_create: Other MPI error, error stack: >> > > MPI_Comm_create(600).................: >> > > MPI_Comm_create(comm=0x84000004, group=0xc800000e, new_comm=0x7fff629d5614) >> > > failed >> > > MPI_Comm_create(577).................: >> > > MPIR_Comm_create_intra(241)..........: >> > > MPIR_Get_contextid(799)..............: >> > > MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >> > > because of fragmentation (2020/2048 free on this process; ignore_id=0) >> > > Fatal error in MPI_Comm_create: Other MPI error, error stack: >> > > MPI_Comm_create(600).................: >> > > MPI_Comm_create(comm=0x84000002, group=0xc8000020, new_comm=0x7fff639ae614) >> > > failed >> > > MPI_Comm_create(577).................: >> > > MPIR_Comm_create_intra(241)..........: >> > > MPIR_Get_contextid(799)..............: >> > > MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >> > > because of fragmentation (2002/2048 free on this process; ignore_id=0 >> > > >> > > Is there a way to fix that ? >> > > >> > > Thanks, >> > > Reem > > >> >> On Mon, Jul 8, 2013 at 9:17 AM, Pavan Balaji <balaji(a)mcs.anl.gov> wrote: >> > >> > Also make sure you are freeing unused communicators. >> > >> > -- Pavan >> > >> > On 07/08/2013 08:14 AM, Wesley Bland wrote: >> >> >> >> It seems that you're creating more communicators than MPICH can handle. >> >> It's possible that you might be able to get around this by setting the >> >> environment variable MPIR_PARAM_CTXID_EAGER_SIZE to something smaller >> >> than >> >> its default (which is 2). That frees up a few more communicators, but >> >> there >> >> is a pathological case where even with fewer communicators than the >> >> max, >> >> MPICH won't be able to agree on a new communicator id when needed. Try >> >> changing that environment variable and see if that fixes things. >> >> >> >> Wesley >> >> >> >> On Jul 8, 2013, at 5:33 AM, Reem Alraddadi <raba500(a)york.ac.uk> wrote: >> >> >> >>> Hi all, >> >>> I am using mpich-3.0.4 on Mac os x version 10.7.5 to run FLASH code. >> >>> It >> >>> works fine in the beginning of the run and then I got the following >> >>> error: >> >>> >> >>> Fatal error in MPI_Comm_create: Other MPI error, error stack: >> >>> MPI_Comm_create(600).................: >> >>> MPI_Comm_create(comm=0x84000002, >> >>> group=0xc8001349, new_comm=0x7fff606a8614) failed >> >>> MPI_Comm_create(577).................: >> >>> MPIR_Comm_create_intra(241)..........: >> >>> MPIR_Get_contextid(799)..............: >> >>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >> >>> because of fragmentation (169/2048 free on this process; ignore_id=0) >> >>> Fatal error in MPI_Comm_create: Other MPI error, error stack: >> >>> MPI_Comm_create(600).................: >> >>> MPI_Comm_create(comm=0x84000002, >> >>> group=0xc80012b6, new_comm=0x7fff670cc614) failed >> >>> MPI_Comm_create(577).................: >> >>> MPIR_Comm_create_intra(241)..........: >> >>> MPIR_Get_contextid(799)..............: >> >>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >> >>> because of fragmentation (316/2048 free on this process; ignore_id=0) >> >>> Fatal error in MPI_Comm_create: Other MPI error, error stack: >> >>> MPI_Comm_create(600).................: >> >>> MPI_Comm_create(comm=0x84000004, >> >>> group=0xc800000e, new_comm=0x7fff629d5614) failed >> >>> MPI_Comm_create(577).................: >> >>> MPIR_Comm_create_intra(241)..........: >> >>> MPIR_Get_contextid(799)..............: >> >>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >> >>> because of fragmentation (2020/2048 free on this process; ignore_id=0) >> >>> Fatal error in MPI_Comm_create: Other MPI error, error stack: >> >>> MPI_Comm_create(600).................: >> >>> MPI_Comm_create(comm=0x84000002, >> >>> group=0xc8000020, new_comm=0x7fff639ae614) failed >> >>> MPI_Comm_create(577).................: >> >>> MPIR_Comm_create_intra(241)..........: >> >>> MPIR_Get_contextid(799)..............: >> >>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >> >>> because of fragmentation (2002/2048 free on this process; ignore_id=0 >> >>> >> >>> Is there a way to fix that ? >> >>> >> >>> Thanks, >> >>> Reem >> >>> _______________________________________________ >> >>> 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 >> >> >> > >> > -- >> > Pavan Balaji >> > http://www.mcs.anl.gov/~balaji >> > _______________________________________________ >> > discuss mailing list discuss(a)mpich.org >> > To manage subscription options or unsubscribe: >> > https://lists.mpich.org/mailman/listinfo/discuss >> >> >> >> -- >> Jeff Hammond >> jeff.science(a)gmail.com >> >> >> ------------------------------ >> >> Message: 3 >> Date: Mon, 8 Jul 2013 16:39:03 +0100 >> From: Reem Alraddadi <raba500(a)york.ac.uk> >> To: discuss(a)mpich.org >> Subject: [mpich-discuss] mpich on Mac os x >> Message-ID: >> >> <CANKsntEJR0b_TA-tbdBO3fOV2O8PkwTG82a718qZPd3FnEBT3w(a)mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi Pavan, >> >> Could you explain more what do you mean by that? I am sorry I am still >> beginner in MPICH. >> >> Hi Wesley, >> apologize about my first confused reply I have forgotten to change the >> subject. However, as I mentioned I wrote the following line: >> >> mpirun --np 4 --env MPIR_PARAM_CTXID_EAGER_SIZE 1 ./flash4 >> >> I am wondering if I made any mistake here as the problem is still the same >> >> Thanks, >> Reem >> >> >> >> Message: 1 >> > Date: Mon, 08 Jul 2013 09:17:00 -0500 >> > From: Pavan Balaji <balaji(a)mcs.anl.gov> >> > To: discuss(a)mpich.org >> > Subject: Re: [mpich-discuss] mpich on Mac os x >> > Message-ID: <51DAC9DC.5000502(a)mcs.anl.gov> >> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> > >> > >> > Also make sure you are freeing unused communicators. >> > >> > -- Pavan >> > >> > On 07/08/2013 08:14 AM, Wesley Bland wrote: >> > > It seems that you're creating more communicators than MPICH can >> > > handle. >> > It's possible that you might be able to get around this by setting the >> > environment variable MPIR_PARAM_CTXID_EAGER_SIZE to something smaller >> > than >> > its default (which is 2). That frees up a few more communicators, but >> > there >> > is a pathological case where even with fewer communicators than the max, >> > MPICH won't be able to agree on a new communicator id when needed. Try >> > changing that environment variable and see if that fixes things. >> > > >> > > Wesley >> > > >> > > On Jul 8, 2013, at 5:33 AM, Reem Alraddadi <raba500(a)york.ac.uk> wrote: >> > > >> > >> Hi all, >> > >> I am using mpich-3.0.4 on Mac os x version 10.7.5 to run FLASH code. >> > >> It >> > works fine in the beginning of the run and then I got the following >> > error: >> > >> >> > >> Fatal error in MPI_Comm_create: Other MPI error, error stack: >> > >> MPI_Comm_create(600).................: >> > >> MPI_Comm_create(comm=0x84000002, >> > group=0xc8001349, new_comm=0x7fff606a8614) failed >> > >> MPI_Comm_create(577).................: >> > >> MPIR_Comm_create_intra(241)..........: >> > >> MPIR_Get_contextid(799)..............: >> > >> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >> > because of fragmentation (169/2048 free on this process; ignore_id=0) >> > >> Fatal error in MPI_Comm_create: Other MPI error, error stack: >> > >> MPI_Comm_create(600).................: >> > >> MPI_Comm_create(comm=0x84000002, >> > group=0xc80012b6, new_comm=0x7fff670cc614) failed >> > >> MPI_Comm_create(577).................: >> > >> MPIR_Comm_create_intra(241)..........: >> > >> MPIR_Get_contextid(799)..............: >> > >> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >> > because of fragmentation (316/2048 free on this process; ignore_id=0) >> > >> Fatal error in MPI_Comm_create: Other MPI error, error stack: >> > >> MPI_Comm_create(600).................: >> > >> MPI_Comm_create(comm=0x84000004, >> > group=0xc800000e, new_comm=0x7fff629d5614) failed >> > >> MPI_Comm_create(577).................: >> > >> MPIR_Comm_create_intra(241)..........: >> > >> MPIR_Get_contextid(799)..............: >> > >> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >> > because of fragmentation (2020/2048 free on this process; ignore_id=0) >> > >> Fatal error in MPI_Comm_create: Other MPI error, error stack: >> > >> MPI_Comm_create(600).................: >> > >> MPI_Comm_create(comm=0x84000002, >> > group=0xc8000020, new_comm=0x7fff639ae614) failed >> > >> MPI_Comm_create(577).................: >> > >> MPIR_Comm_create_intra(241)..........: >> > >> MPIR_Get_contextid(799)..............: >> > >> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID >> > because of fragmentation (2002/2048 free on this process; ignore_id=0 >> > >> >> > >> Is there a way to fix that ? >> > >> >> > >> Thanks, >> > >> Reem >> > >> _______________________________________________ >> > >> 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 >> > > >> > >> > -- >> > Pavan Balaji >> > http://www.mcs.anl.gov/~balaji >> > >>

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