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

Re: [mpich-discuss] Getting an undeclared error on compile, with mpicc
by Kenneth Raffenetti 01 May '14

01 May '14

How was MPICH installed? Are you including the right mpi.h header in your program? Have you tried compiling and running the cpi.c example that comes with MPICH? If you send us the smallest possible program that can reproduce this error, it would help us get to the bottom of the issue. Ken On 05/01/2014 09:49 AM, mark wrote: > Hello. > I am getting an error that i wasn't getting before. > > ------------------------------------------------------------------------ > test.c: In function 'main': > test.c:63: error: 'MPI_COMM_WORLD' undeclared (first use in this function) > test.c:63: error: (Each undeclared identifier is reported only once > test.c:63: error: for each function it appears in.) > test.c:111: error: 'MPI_INT' undeclared (first use in this function) > ------------------------------------------------------------------------ > line 63 : MPI_Comm_size(MPI_COMM_WORLD, &numnodes); > line 111:MPI_Scatter( array, PARTS, MPI_INT, my_array, PARTS, MPI_INT, > master, MPI_COMM_WORLD); > > > I am under a 2.6.23-gentoo-r5 cluster with gcc version 4.2.2 (Gentoo > 4.2.2 p1.0) > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss >

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Getting an undeclared error on compile, with mpicc
by mark 01 May '14

01 May '14

Hello. I am getting an error that i wasn't getting before. ------------------------------------------------------------------------ test.c: In function 'main': test.c:63: error: 'MPI_COMM_WORLD' undeclared (first use in this function) test.c:63: error: (Each undeclared identifier is reported only once test.c:63: error: for each function it appears in.) test.c:111: error: 'MPI_INT' undeclared (first use in this function) ------------------------------------------------------------------------ line 63 : MPI_Comm_size(MPI_COMM_WORLD, &numnodes); line 111:MPI_Scatter( array, PARTS, MPI_INT, my_array, PARTS, MPI_INT, master, MPI_COMM_WORLD); I am under a 2.6.23-gentoo-r5 cluster with gcc version 4.2.2 (Gentoo 4.2.2 p1.0)

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Re: [mpich-discuss] Memory leak comparing communicators
by VandeVondele Joost 01 May '14

01 May '14

actually, the issue seems to be with MPI_Comm_group since translate_ranks can be just commented out. Joost ________________________________________ From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf of "Antonio J. Peña" [apenya(a)mcs.anl.gov] Sent: Thursday, May 01, 2014 4:08 PM To: discuss(a)mpich.org Subject: Re: [mpich-discuss] Memory leak comparing communicators Thank you Joost. We'll check this issue. I'll keep you posted. On 05/01/2014 09:02 AM, VandeVondele Joost wrote: > Hi Antonio, > > I finally reproduced this in a small program. The culprit actually seems to be MPI_Group_translate_ranks, but the leak shows up with a trace to MPI_Comm_compare: > > Direct leak of 3072 byte(s) in 96 object(s) allocated from: > #0 0x7fdab2e213a8 in __interceptor_malloc ../../../../gcc/libsanitizer/lsan/lsan_interceptors.cc:66 > #1 0x7fdab3efaf6b in MPIR_Group_create /data/vjoost/mpich-3.1/src/mpi/group/grouputil.c:77 > #2 0x7fdab3fc8314 in MPIR_Comm_group_impl /data/vjoost/mpich-3.1/src/mpi/comm/comm_group.c:44 > #3 0x7fdab3fc40d3 in PMPI_Comm_compare /data/vjoost/mpich-3.1/src/mpi/comm/comm_compare.c:122 > #4 0x4009de in main /data/vjoost/mpich-3.1/debug/2d.c:23 > >> cat 2d.c > #include <stdio.h> > #include <mpi.h> > > main(int argc, char **argv) // needs 2 ranks // > { > MPI_Comm comm_cart, dup_comm_world; > int result,reorder; > int dim[2], period[2], rin[2], rout[2]; > int i,j,k; > int g1,g2; > > MPI_Init (&argc, &argv); > > for(i=0;i<100;i++) > { > > MPI_Comm_dup( MPI_COMM_WORLD, &dup_comm_world); > dim[0]=2; dim[1]=1; > reorder=0; > period[0]=1; period[1]=1; > rin[0]=0; rin[1]=1; > MPI_Cart_create(dup_comm_world, 2, dim, period, reorder, &comm_cart); > MPI_Comm_compare(dup_comm_world, comm_cart, &result ); > MPI_Comm_group(dup_comm_world,&g1); > MPI_Comm_group(comm_cart,&g2); > MPI_Group_translate_ranks(g1, 2, rin, g2, rout); > MPI_Comm_free(&comm_cart); > MPI_Comm_free(&dup_comm_world); > > } > > MPI_Finalize(); > > } > > Thanks, > > Joost > > > > > ________________________________________ > From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf of "Antonio J. Peña" [apenya(a)mcs.anl.gov] > Sent: Monday, April 28, 2014 6:26 PM > To: discuss(a)mpich.org > Subject: Re: [mpich-discuss] Memory leak comparing communicators > > Hi Joost, > > Can you share the smallest fragment of code with which we can reproduce > this? > > Antonio > > > On 04/28/2014 11:25 AM, VandeVondele Joost wrote: >> Hi, >> >> using mpich 3.1 I notice that my application leaks memory. Compiling it with '-O1 -g -fno-omit-frame-pointer -fsanitize=leak' using gcc 4.9 it appears the sources is comparing communicators, for example: >> >> [0] Direct leak of 38400 byte(s) in 600 object(s) allocated from: >> [0] #0 0x7f84298d53a8 in __interceptor_malloc ../../../../gcc/libsanitizer/lsan/lsan_interceptors.cc:66 >> [0] #1 0x7f842aabaf6b in MPIR_Group_create /data/vjoost/mpich-3.1/src/mpi/group/grouputil.c:77 >> [0] #2 0x7f842ab88314 in MPIR_Comm_group_impl /data/vjoost/mpich-3.1/src/mpi/comm/comm_group.c:44 >> [0] #3 0x7f842ab840d3 in PMPI_Comm_compare /data/vjoost/mpich-3.1/src/mpi/comm/comm_compare.c:122 >> [0] #4 0x7f842aac8e84 in pmpi_comm_compare_ /data/vjoost/mpich-3.1/src/binding/f77/comm_comparef.c:267 >> [0] #5 0x1bfd447 in __message_passing_MOD_mp_comm_compare /data/vjoost/clean/cp2k/cp2k/src/common/message_passing.F:1084 >> >> I'm not seeing other leaks, so is guess something particular is going on here. Any suggestions on a possible fix ? >> >> Thanks, >> >> Joost >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss > > -- > 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 > apenya(a)mcs.anl.gov > www.mcs.anl.gov/~apenya > > _______________________________________________ > 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 -- 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 apenya(a)mcs.anl.gov www.mcs.anl.gov/~apenya _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] Memory leak comparing communicators
by "Antonio J. Peña" 01 May '14

01 May '14

Haven't had time yet. It's coming... On 05/01/2014 09:18 AM, Rob Latham wrote: > > > On 05/01/2014 09:08 AM, "Antonio J. Peï¿½a" wrote: >> >> Thank you Joost. We'll check this issue. I'll keep you posted. > > what's the trac ticket for this issue? > > ==rob > >> >> >> On 05/01/2014 09:02 AM, VandeVondele Joost wrote: >>> Hi Antonio, >>> >>> I finally reproduced this in a small program. The culprit actually >>> seems to be MPI_Group_translate_ranks, but the leak shows up with a >>> trace to MPI_Comm_compare: >>> >>> Direct leak of 3072 byte(s) in 96 object(s) allocated from: >>> #0 0x7fdab2e213a8 in __interceptor_malloc >>> ../../../../gcc/libsanitizer/lsan/lsan_interceptors.cc:66 >>> #1 0x7fdab3efaf6b in MPIR_Group_create >>> /data/vjoost/mpich-3.1/src/mpi/group/grouputil.c:77 >>> #2 0x7fdab3fc8314 in MPIR_Comm_group_impl >>> /data/vjoost/mpich-3.1/src/mpi/comm/comm_group.c:44 >>> #3 0x7fdab3fc40d3 in PMPI_Comm_compare >>> /data/vjoost/mpich-3.1/src/mpi/comm/comm_compare.c:122 >>> #4 0x4009de in main /data/vjoost/mpich-3.1/debug/2d.c:23 >>> >>>> cat 2d.c >>> #include <stdio.h> >>> #include <mpi.h> >>> >>> main(int argc, char **argv) // needs 2 ranks // >>> { >>> MPI_Comm comm_cart, dup_comm_world; >>> int result,reorder; >>> int dim[2], period[2], rin[2], rout[2]; >>> int i,j,k; >>> int g1,g2; >>> >>> MPI_Init (&argc, &argv); >>> >>> for(i=0;i<100;i++) >>> { >>> >>> MPI_Comm_dup( MPI_COMM_WORLD, &dup_comm_world); >>> dim[0]=2; dim[1]=1; >>> reorder=0; >>> period[0]=1; period[1]=1; >>> rin[0]=0; rin[1]=1; >>> MPI_Cart_create(dup_comm_world, 2, dim, period, reorder, >>> &comm_cart); >>> MPI_Comm_compare(dup_comm_world, comm_cart, &result ); >>> MPI_Comm_group(dup_comm_world,&g1); >>> MPI_Comm_group(comm_cart,&g2); >>> MPI_Group_translate_ranks(g1, 2, rin, g2, rout); >>> MPI_Comm_free(&comm_cart); >>> MPI_Comm_free(&dup_comm_world); >>> >>> } >>> >>> MPI_Finalize(); >>> >>> } >>> >>> Thanks, >>> >>> Joost >>> >>> >>> >>> >>> ________________________________________ >>> From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf >>> of "Antonio J. Peï¿½a" [apenya(a)mcs.anl.gov] >>> Sent: Monday, April 28, 2014 6:26 PM >>> To: discuss(a)mpich.org >>> Subject: Re: [mpich-discuss] Memory leak comparing communicators >>> >>> Hi Joost, >>> >>> Can you share the smallest fragment of code with which we can reproduce >>> this? >>> >>> Antonio >>> >>> >>> On 04/28/2014 11:25 AM, VandeVondele Joost wrote: >>>> Hi, >>>> >>>> using mpich 3.1 I notice that my application leaks memory. Compiling >>>> it with '-O1 -g -fno-omit-frame-pointer -fsanitize=leak' using gcc >>>> 4.9 it appears the sources is comparing communicators, for example: >>>> >>>> [0] Direct leak of 38400 byte(s) in 600 object(s) allocated from: >>>> [0] #0 0x7f84298d53a8 in __interceptor_malloc >>>> ../../../../gcc/libsanitizer/lsan/lsan_interceptors.cc:66 >>>> [0] #1 0x7f842aabaf6b in MPIR_Group_create >>>> /data/vjoost/mpich-3.1/src/mpi/group/grouputil.c:77 >>>> [0] #2 0x7f842ab88314 in MPIR_Comm_group_impl >>>> /data/vjoost/mpich-3.1/src/mpi/comm/comm_group.c:44 >>>> [0] #3 0x7f842ab840d3 in PMPI_Comm_compare >>>> /data/vjoost/mpich-3.1/src/mpi/comm/comm_compare.c:122 >>>> [0] #4 0x7f842aac8e84 in pmpi_comm_compare_ >>>> /data/vjoost/mpich-3.1/src/binding/f77/comm_comparef.c:267 >>>> [0] #5 0x1bfd447 in __message_passing_MOD_mp_comm_compare >>>> /data/vjoost/clean/cp2k/cp2k/src/common/message_passing.F:1084 >>>> >>>> I'm not seeing other leaks, so is guess something particular is going >>>> on here. Any suggestions on a possible fix ? >>>> >>>> Thanks, >>>> >>>> Joost >>>> _______________________________________________ >>>> discuss mailing list discuss(a)mpich.org >>>> To manage subscription options or unsubscribe: >>>> https://lists.mpich.org/mailman/listinfo/discuss >>> >>> -- >>> Antonio J. Peï¿½a >>> Postdoctoral Appointee >>> Mathematics and Computer Science Division >>> Argonne National Laboratory >>> 9700 South Cass Avenue, Bldg. 240, Of. 3148 >>> Argonne, IL 60439-4847 >>> apenya(a)mcs.anl.gov >>> www.mcs.anl.gov/~apenya >>> >>> _______________________________________________ >>> 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 >> >> > -- Antonio J. Peï¿½a Postdoctoral Appointee Mathematics and Computer Science Division Argonne National Laboratory 9700 South Cass Avenue, Bldg. 240, Of. 3148 Argonne, IL 60439-4847 apenya(a)mcs.anl.gov www.mcs.anl.gov/~apenya

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Re: [mpich-discuss] Memory leak comparing communicators
by Rob Latham 01 May '14

01 May '14

On 05/01/2014 09:08 AM, "Antonio J. Peï¿½a" wrote: > > Thank you Joost. We'll check this issue. I'll keep you posted. what's the trac ticket for this issue? ==rob > > > On 05/01/2014 09:02 AM, VandeVondele Joost wrote: >> Hi Antonio, >> >> I finally reproduced this in a small program. The culprit actually >> seems to be MPI_Group_translate_ranks, but the leak shows up with a >> trace to MPI_Comm_compare: >> >> Direct leak of 3072 byte(s) in 96 object(s) allocated from: >> #0 0x7fdab2e213a8 in __interceptor_malloc >> ../../../../gcc/libsanitizer/lsan/lsan_interceptors.cc:66 >> #1 0x7fdab3efaf6b in MPIR_Group_create >> /data/vjoost/mpich-3.1/src/mpi/group/grouputil.c:77 >> #2 0x7fdab3fc8314 in MPIR_Comm_group_impl >> /data/vjoost/mpich-3.1/src/mpi/comm/comm_group.c:44 >> #3 0x7fdab3fc40d3 in PMPI_Comm_compare >> /data/vjoost/mpich-3.1/src/mpi/comm/comm_compare.c:122 >> #4 0x4009de in main /data/vjoost/mpich-3.1/debug/2d.c:23 >> >>> cat 2d.c >> #include <stdio.h> >> #include <mpi.h> >> >> main(int argc, char **argv) // needs 2 ranks // >> { >> MPI_Comm comm_cart, dup_comm_world; >> int result,reorder; >> int dim[2], period[2], rin[2], rout[2]; >> int i,j,k; >> int g1,g2; >> >> MPI_Init (&argc, &argv); >> >> for(i=0;i<100;i++) >> { >> >> MPI_Comm_dup( MPI_COMM_WORLD, &dup_comm_world); >> dim[0]=2; dim[1]=1; >> reorder=0; >> period[0]=1; period[1]=1; >> rin[0]=0; rin[1]=1; >> MPI_Cart_create(dup_comm_world, 2, dim, period, reorder, >> &comm_cart); >> MPI_Comm_compare(dup_comm_world, comm_cart, &result ); >> MPI_Comm_group(dup_comm_world,&g1); >> MPI_Comm_group(comm_cart,&g2); >> MPI_Group_translate_ranks(g1, 2, rin, g2, rout); >> MPI_Comm_free(&comm_cart); >> MPI_Comm_free(&dup_comm_world); >> >> } >> >> MPI_Finalize(); >> >> } >> >> Thanks, >> >> Joost >> >> >> >> >> ________________________________________ >> From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf >> of "Antonio J. Peï¿½a" [apenya(a)mcs.anl.gov] >> Sent: Monday, April 28, 2014 6:26 PM >> To: discuss(a)mpich.org >> Subject: Re: [mpich-discuss] Memory leak comparing communicators >> >> Hi Joost, >> >> Can you share the smallest fragment of code with which we can reproduce >> this? >> >> Antonio >> >> >> On 04/28/2014 11:25 AM, VandeVondele Joost wrote: >>> Hi, >>> >>> using mpich 3.1 I notice that my application leaks memory. Compiling >>> it with '-O1 -g -fno-omit-frame-pointer -fsanitize=leak' using gcc >>> 4.9 it appears the sources is comparing communicators, for example: >>> >>> [0] Direct leak of 38400 byte(s) in 600 object(s) allocated from: >>> [0] #0 0x7f84298d53a8 in __interceptor_malloc >>> ../../../../gcc/libsanitizer/lsan/lsan_interceptors.cc:66 >>> [0] #1 0x7f842aabaf6b in MPIR_Group_create >>> /data/vjoost/mpich-3.1/src/mpi/group/grouputil.c:77 >>> [0] #2 0x7f842ab88314 in MPIR_Comm_group_impl >>> /data/vjoost/mpich-3.1/src/mpi/comm/comm_group.c:44 >>> [0] #3 0x7f842ab840d3 in PMPI_Comm_compare >>> /data/vjoost/mpich-3.1/src/mpi/comm/comm_compare.c:122 >>> [0] #4 0x7f842aac8e84 in pmpi_comm_compare_ >>> /data/vjoost/mpich-3.1/src/binding/f77/comm_comparef.c:267 >>> [0] #5 0x1bfd447 in __message_passing_MOD_mp_comm_compare >>> /data/vjoost/clean/cp2k/cp2k/src/common/message_passing.F:1084 >>> >>> I'm not seeing other leaks, so is guess something particular is going >>> on here. Any suggestions on a possible fix ? >>> >>> Thanks, >>> >>> Joost >>> _______________________________________________ >>> discuss mailing list discuss(a)mpich.org >>> To manage subscription options or unsubscribe: >>> https://lists.mpich.org/mailman/listinfo/discuss >> >> -- >> Antonio J. Peï¿½a >> Postdoctoral Appointee >> Mathematics and Computer Science Division >> Argonne National Laboratory >> 9700 South Cass Avenue, Bldg. 240, Of. 3148 >> Argonne, IL 60439-4847 >> apenya(a)mcs.anl.gov >> www.mcs.anl.gov/~apenya >> >> _______________________________________________ >> 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 > > -- Rob Latham Mathematics and Computer Science Division Argonne National Lab, IL USA

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Re: [mpich-discuss] Memory leak comparing communicators
by "Antonio J. Peña" 01 May '14

01 May '14

Thank you Joost. We'll check this issue. I'll keep you posted. On 05/01/2014 09:02 AM, VandeVondele Joost wrote: > Hi Antonio, > > I finally reproduced this in a small program. The culprit actually seems to be MPI_Group_translate_ranks, but the leak shows up with a trace to MPI_Comm_compare: > > Direct leak of 3072 byte(s) in 96 object(s) allocated from: > #0 0x7fdab2e213a8 in __interceptor_malloc ../../../../gcc/libsanitizer/lsan/lsan_interceptors.cc:66 > #1 0x7fdab3efaf6b in MPIR_Group_create /data/vjoost/mpich-3.1/src/mpi/group/grouputil.c:77 > #2 0x7fdab3fc8314 in MPIR_Comm_group_impl /data/vjoost/mpich-3.1/src/mpi/comm/comm_group.c:44 > #3 0x7fdab3fc40d3 in PMPI_Comm_compare /data/vjoost/mpich-3.1/src/mpi/comm/comm_compare.c:122 > #4 0x4009de in main /data/vjoost/mpich-3.1/debug/2d.c:23 > >> cat 2d.c > #include <stdio.h> > #include <mpi.h> > > main(int argc, char **argv) // needs 2 ranks // > { > MPI_Comm comm_cart, dup_comm_world; > int result,reorder; > int dim[2], period[2], rin[2], rout[2]; > int i,j,k; > int g1,g2; > > MPI_Init (&argc, &argv); > > for(i=0;i<100;i++) > { > > MPI_Comm_dup( MPI_COMM_WORLD, &dup_comm_world); > dim[0]=2; dim[1]=1; > reorder=0; > period[0]=1; period[1]=1; > rin[0]=0; rin[1]=1; > MPI_Cart_create(dup_comm_world, 2, dim, period, reorder, &comm_cart); > MPI_Comm_compare(dup_comm_world, comm_cart, &result ); > MPI_Comm_group(dup_comm_world,&g1); > MPI_Comm_group(comm_cart,&g2); > MPI_Group_translate_ranks(g1, 2, rin, g2, rout); > MPI_Comm_free(&comm_cart); > MPI_Comm_free(&dup_comm_world); > > } > > MPI_Finalize(); > > } > > Thanks, > > Joost > > > > > ________________________________________ > From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf of "Antonio J. Peï¿½a" [apenya(a)mcs.anl.gov] > Sent: Monday, April 28, 2014 6:26 PM > To: discuss(a)mpich.org > Subject: Re: [mpich-discuss] Memory leak comparing communicators > > Hi Joost, > > Can you share the smallest fragment of code with which we can reproduce > this? > > Antonio > > > On 04/28/2014 11:25 AM, VandeVondele Joost wrote: >> Hi, >> >> using mpich 3.1 I notice that my application leaks memory. Compiling it with '-O1 -g -fno-omit-frame-pointer -fsanitize=leak' using gcc 4.9 it appears the sources is comparing communicators, for example: >> >> [0] Direct leak of 38400 byte(s) in 600 object(s) allocated from: >> [0] #0 0x7f84298d53a8 in __interceptor_malloc ../../../../gcc/libsanitizer/lsan/lsan_interceptors.cc:66 >> [0] #1 0x7f842aabaf6b in MPIR_Group_create /data/vjoost/mpich-3.1/src/mpi/group/grouputil.c:77 >> [0] #2 0x7f842ab88314 in MPIR_Comm_group_impl /data/vjoost/mpich-3.1/src/mpi/comm/comm_group.c:44 >> [0] #3 0x7f842ab840d3 in PMPI_Comm_compare /data/vjoost/mpich-3.1/src/mpi/comm/comm_compare.c:122 >> [0] #4 0x7f842aac8e84 in pmpi_comm_compare_ /data/vjoost/mpich-3.1/src/binding/f77/comm_comparef.c:267 >> [0] #5 0x1bfd447 in __message_passing_MOD_mp_comm_compare /data/vjoost/clean/cp2k/cp2k/src/common/message_passing.F:1084 >> >> I'm not seeing other leaks, so is guess something particular is going on here. Any suggestions on a possible fix ? >> >> Thanks, >> >> Joost >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss > > -- > Antonio J. Peï¿½a > Postdoctoral Appointee > Mathematics and Computer Science Division > Argonne National Laboratory > 9700 South Cass Avenue, Bldg. 240, Of. 3148 > Argonne, IL 60439-4847 > apenya(a)mcs.anl.gov > www.mcs.anl.gov/~apenya > > _______________________________________________ > 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 -- Antonio J. Peï¿½a Postdoctoral Appointee Mathematics and Computer Science Division Argonne National Laboratory 9700 South Cass Avenue, Bldg. 240, Of. 3148 Argonne, IL 60439-4847 apenya(a)mcs.anl.gov www.mcs.anl.gov/~apenya

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Re: [mpich-discuss] Memory leak comparing communicators
by VandeVondele Joost 01 May '14

01 May '14

Hi Antonio, I finally reproduced this in a small program. The culprit actually seems to be MPI_Group_translate_ranks, but the leak shows up with a trace to MPI_Comm_compare: Direct leak of 3072 byte(s) in 96 object(s) allocated from: #0 0x7fdab2e213a8 in __interceptor_malloc ../../../../gcc/libsanitizer/lsan/lsan_interceptors.cc:66 #1 0x7fdab3efaf6b in MPIR_Group_create /data/vjoost/mpich-3.1/src/mpi/group/grouputil.c:77 #2 0x7fdab3fc8314 in MPIR_Comm_group_impl /data/vjoost/mpich-3.1/src/mpi/comm/comm_group.c:44 #3 0x7fdab3fc40d3 in PMPI_Comm_compare /data/vjoost/mpich-3.1/src/mpi/comm/comm_compare.c:122 #4 0x4009de in main /data/vjoost/mpich-3.1/debug/2d.c:23 > cat 2d.c #include <stdio.h> #include <mpi.h> main(int argc, char **argv) // needs 2 ranks // { MPI_Comm comm_cart, dup_comm_world; int result,reorder; int dim[2], period[2], rin[2], rout[2]; int i,j,k; int g1,g2; MPI_Init (&argc, &argv); for(i=0;i<100;i++) { MPI_Comm_dup( MPI_COMM_WORLD, &dup_comm_world); dim[0]=2; dim[1]=1; reorder=0; period[0]=1; period[1]=1; rin[0]=0; rin[1]=1; MPI_Cart_create(dup_comm_world, 2, dim, period, reorder, &comm_cart); MPI_Comm_compare(dup_comm_world, comm_cart, &result ); MPI_Comm_group(dup_comm_world,&g1); MPI_Comm_group(comm_cart,&g2); MPI_Group_translate_ranks(g1, 2, rin, g2, rout); MPI_Comm_free(&comm_cart); MPI_Comm_free(&dup_comm_world); } MPI_Finalize(); } Thanks, Joost ________________________________________ From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf of "Antonio J. Peña" [apenya(a)mcs.anl.gov] Sent: Monday, April 28, 2014 6:26 PM To: discuss(a)mpich.org Subject: Re: [mpich-discuss] Memory leak comparing communicators Hi Joost, Can you share the smallest fragment of code with which we can reproduce this? Antonio On 04/28/2014 11:25 AM, VandeVondele Joost wrote: > Hi, > > using mpich 3.1 I notice that my application leaks memory. Compiling it with '-O1 -g -fno-omit-frame-pointer -fsanitize=leak' using gcc 4.9 it appears the sources is comparing communicators, for example: > > [0] Direct leak of 38400 byte(s) in 600 object(s) allocated from: > [0] #0 0x7f84298d53a8 in __interceptor_malloc ../../../../gcc/libsanitizer/lsan/lsan_interceptors.cc:66 > [0] #1 0x7f842aabaf6b in MPIR_Group_create /data/vjoost/mpich-3.1/src/mpi/group/grouputil.c:77 > [0] #2 0x7f842ab88314 in MPIR_Comm_group_impl /data/vjoost/mpich-3.1/src/mpi/comm/comm_group.c:44 > [0] #3 0x7f842ab840d3 in PMPI_Comm_compare /data/vjoost/mpich-3.1/src/mpi/comm/comm_compare.c:122 > [0] #4 0x7f842aac8e84 in pmpi_comm_compare_ /data/vjoost/mpich-3.1/src/binding/f77/comm_comparef.c:267 > [0] #5 0x1bfd447 in __message_passing_MOD_mp_comm_compare /data/vjoost/clean/cp2k/cp2k/src/common/message_passing.F:1084 > > I'm not seeing other leaks, so is guess something particular is going on here. Any suggestions on a possible fix ? > > Thanks, > > Joost > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- 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 apenya(a)mcs.anl.gov www.mcs.anl.gov/~apenya _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] error class MPI_ERR_NO_SUCH_FILE thrown by MPI_File_delete
by Rob Latham 01 May '14

01 May '14

On 04/05/2014 02:48 PM, Wei-keng Liao wrote: > In MPI-2 standard has the sentence below for MPI_File_delete. > "If the file does not exist, MPI_FILE_DELETE raises an error in the class MPI_ERR_NO_SUCH_FILE." this is now ticket http://trac.mpich.org/projects/mpich/ticket/2075. I think I can fix this today. ==rob > > But in src/mpi/romio/adio/common/ad_delete.c, the return code of unlink() is not checked > for this error (only MPI_ERR_IO class is thrown.) May I suggest to add a check, so the > MPI_ERR_NO_SUCH_FILE class can reported. > > 19 err = unlink(filename); > if (err == ENOENT) { > *error_code = MPIO_Err_create_code(MPI_SUCCESS, MPIR_ERR_RECOVERABLE, > myname, __LINE__, MPI_ERR_NO_SUCH_FILE, "**io", > "**io %s", strerror(errno)); > return; > } > else if (err == -1) { > ... -- Rob Latham Mathematics and Computer Science Division Argonne National Lab, IL USA

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