July 2015 - discuss - mailman3.cels.anl.gov

resized2.c issues
by Michael L. Stokes 31 Jul '15

31 Jul '15

I'm running mpich-3.1.2/test/mpi/io/resized2 with the output file size is 20, should be 16 newbuf[0] is 55, should be 10, newbuf[1] is 10, should be 55, newbuf[2] is 55, should be 55, newbuf[3] is 55, should be 20 Found 2 errors I have run this test case across a number of machines. It is listed as belonging to ticket2088. Can anyone tell me if this is an unresolved issue or some error on my part? Thanks Mike _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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question about valgrind errors I am getting
by Grindeanu, Iulian R. 31 Jul '15

31 Jul '15

hello, I am trying to see where is the leak in our code; valgrind shows some leaks, like these ==4262== 1,512 bytes in 3 blocks are still reachable in loss record 6 of 6 ==4262== at 0x4C2CC70: calloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so) ==4262== by 0x56A6555: set_collops.part.0 (in /home/iulian/3rdparty/mpich-3.1/install/lib/libmpich.so.12.0.0) ==4262== by 0x56A73E2: MPIR_Comm_commit (in /home/iulian/3rdparty/mpich-3.1/install/lib/libmpich.so.12.0.0) ==4262== by 0x56DFAD3: MPID_Init (in /home/iulian/3rdparty/mpich-3.1/install/lib/libmpich.so.12.0.0) ==4262== by 0x5796878: MPIR_Init_thread (in /home/iulian/3rdparty/mpich-3.1/install/lib/libmpich.so.12.0.0) ==4262== by 0x5796288: PMPI_Init (in /home/iulian/3rdparty/mpich-3.1/install/lib/libmpich.so.12.0.0) ==4262== by 0x40B20B: main (read_nc.cpp:18) in our code, line 18 is MPI_Init(..) commenting out portions of our code gets rid of the leaks; do you have a suggestion what are we doing wrong, or what is the leak related to? Or could it be a false positive from valgrind? Thanks, Iulian _______________________________________________ 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] Nemesis engine query by Viswanath
by Halim Amer 31 Jul '15

31 Jul '15

You can learn more about multithreading support in MPI from the standard (www.mpi-forum.org/docs/mpi-3.1/mpi31-report.pdf) in section 12.4. If you need us to help, we need more information such as configure line, target platform, compiler version, and most importantly, a toy program that reproduces the bug. --Halim On 7/31/15 4:41 AM, Viswanath Krishnamurthy wrote: > I did try initializing Multithreading support > #include<mpi.h> > int main() > { > > int provided; > int returnvalue = > MPI_Init_thread(&argc,&argv,MPI_THREAD_MULTIPLE,&provided); > if(provided < MPI_THREAD_MULTIPLE) > { > printf("\n THREAD LIBRARY DOESN'T HAVE MULTITHREADING > SUPPORT:"); > exit(1); > } > } > > The code compiles but throws an error - > Assertion failed in file > /home/viswa/libraries/mpich-3.1.4/src/include/mpiimplthreadpost.h at > line 163: depth > 0 && depth < 10 > internal ABORT - process 1 > internal ABORT - process 0 > > Could you please refer me to some documentation for mpi_init_thread/ > MPICH-multithreading documentation as I am relatively new to it. > > Thanks, > Viswanath > > > > On Fri, Jul 31, 2015 at 2:41 AM, <discuss-request(a)mpich.org > <mailto:[email protected]>> wrote: > > Send discuss mailing list submissions to > discuss(a)mpich.org <mailto:[email protected]> > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.mpich.org/mailman/listinfo/discuss > or, via email, send a message with subject or body 'help' to > discuss-request(a)mpich.org <mailto:[email protected]> > > You can reach the person managing the list at > discuss-owner(a)mpich.org <mailto:[email protected]> > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of discuss digest..." > > > Today's Topics: > > 1. PANFS Remove RAID0 and add RAIDN to MPICH 3.2 (Victorelli, Ron) > 2. Re: PANFS Remove RAID0 and add RAIDN to MPICH 3.2 (Rob Latham) > 3. Re: hydra, stdin close(), and SLURM (Aaron Knister) > 4. Re: Nemesis engine (Viswanath Krishnamurthy) > 5. Re: Nemesis engine (Halim Amer) > 6. Active loop in MPI_Waitany? (Dorier, Matthieu) > 7. Re: Active loop in MPI_Waitany? (Jeff Hammond) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 29 Jul 2015 12:07:40 +0000 > From: "Victorelli, Ron" <rvictorelli(a)panasas.com > <mailto:[email protected]>> > To: "discuss(a)mpich.org <mailto:[email protected]>" > <discuss(a)mpich.org <mailto:[email protected]>> > Subject: [mpich-discuss] PANFS Remove RAID0 and add RAIDN to MPICH 3.2 > Message-ID: > > <BN3PR08MB12888AACA7907A8ACED7531AA18C0(a)BN3PR08MB1288.namprd08.prod.outlook.com > <mailto:BN3PR08MB12888AACA7907A8ACED7531AA18C0@BN3PR08MB1288.namprd08.prod.outlook.com>> > > Content-Type: text/plain; charset="us-ascii" > > I am a developer at Panasas, and we would like to provide a patch that > removes RAID0 support and adds RAIDN support to romio (MPICH 3.2): > > src/mpi/romio/adio/ad_panfs/ad_panfs_open.c > > I currently do not have an MCS or trac account. > > Thank You > > Ron Victorelli > Software Engineer > Panasas, Inc > Email: rvictorelli(a)panasas.com > <mailto:[email protected]><mailto:[email protected] > <mailto:[email protected]>> > Tel: 412 -323-6422 <tel:412%20-323-6422> > www.panasas.com <http://www.panasas.com><http://www.panasas.com> > [Panasas_Logo_LR] >

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Re: [mpich-discuss] Nemesis engine query by Viswanath
by Viswanath Krishnamurthy 31 Jul '15

31 Jul '15

I did try initializing Multithreading support #include<mpi.h> int main() { int provided; int returnvalue = MPI_Init_thread(&argc,&argv,MPI_THREAD_MULTIPLE,&provided); if(provided < MPI_THREAD_MULTIPLE) { printf("\n THREAD LIBRARY DOESN'T HAVE MULTITHREADING SUPPORT:"); exit(1); } } The code compiles but throws an error - Assertion failed in file /home/viswa/libraries/mpich-3.1.4/src/include/mpiimplthreadpost.h at line 163: depth > 0 && depth < 10 internal ABORT - process 1 internal ABORT - process 0 Could you please refer me to some documentation for mpi_init_thread/ MPICH-multithreading documentation as I am relatively new to it. Thanks, Viswanath On Fri, Jul 31, 2015 at 2:41 AM, <discuss-request(a)mpich.org> wrote: > Send discuss mailing list submissions to > discuss(a)mpich.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.mpich.org/mailman/listinfo/discuss > or, via email, send a message with subject or body 'help' to > discuss-request(a)mpich.org > > You can reach the person managing the list at > discuss-owner(a)mpich.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of discuss digest..." > > > Today's Topics: > > 1. PANFS Remove RAID0 and add RAIDN to MPICH 3.2 (Victorelli, Ron) > 2. Re: PANFS Remove RAID0 and add RAIDN to MPICH 3.2 (Rob Latham) > 3. Re: hydra, stdin close(), and SLURM (Aaron Knister) > 4. Re: Nemesis engine (Viswanath Krishnamurthy) > 5. Re: Nemesis engine (Halim Amer) > 6. Active loop in MPI_Waitany? (Dorier, Matthieu) > 7. Re: Active loop in MPI_Waitany? (Jeff Hammond) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 29 Jul 2015 12:07:40 +0000 > From: "Victorelli, Ron" <rvictorelli(a)panasas.com> > To: "discuss(a)mpich.org" <discuss(a)mpich.org> > Subject: [mpich-discuss] PANFS Remove RAID0 and add RAIDN to MPICH 3.2 > Message-ID: > < > BN3PR08MB12888AACA7907A8ACED7531AA18C0(a)BN3PR08MB1288.namprd08.prod.outlook.com > > > > Content-Type: text/plain; charset="us-ascii" > > I am a developer at Panasas, and we would like to provide a patch that > removes RAID0 support and adds RAIDN support to romio (MPICH 3.2): > > src/mpi/romio/adio/ad_panfs/ad_panfs_open.c > > I currently do not have an MCS or trac account. > > Thank You > > Ron Victorelli > Software Engineer > Panasas, Inc > Email: rvictorelli(a)panasas.com<mailto:[email protected]> > Tel: 412 -323-6422 > www.panasas.com<http://www.panasas.com> > [Panasas_Logo_LR] > _______________________________________________ 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] Active loop in MPI_Waitany?
by Jeff Hammond 30 Jul '15

30 Jul '15

Everyone on this list doesn't know the guts of nemesis?!?!? :-) Jeff PS ch3:sock might give you different results ;-) On Thursday, July 30, 2015, Dorier, Matthieu <mdorier(a)anl.gov> wrote: > Not that obvious, a UNIX function like "select" would allow to block on a > set of file descriptors (for instance sockets), so I was expecting > MPI_Waitany to work kind of the same way. Pavan explained me (in person) > why it does not: it cannot at the same time block on a read from shared > memory (channels inside a node) and on network connections (outside the > node). (I'm simplifying a bit here). > > So the answer is: yes, MPI_Waitany is actively looping. > > Matthieu > > ------------------------------ > *From:* Jeff Hammond [jeff.science(a)gmail.com > <javascript:_e(%7B%7D,'cvml','jeff.science(a)gmail.com');>] > *Sent:* Thursday, July 30, 2015 6:41 PM > *To:* discuss(a)mpich.org > <javascript:_e(%7B%7D,'cvml','discuss(a)mpich.org');> > *Subject:* Re: [mpich-discuss] Active loop in MPI_Waitany? > > Seems obvious that Waitany spins on the array of requests until one > completes. Is that an active loop by your definition? > > Jeff > > On Thursday, July 30, 2015, Dorier, Matthieu <mdorier(a)anl.gov > <javascript:_e(%7B%7D,'cvml','mdorier(a)anl.gov');>> wrote: > >> Hi, >> >> I have a code that looks like this: >> >> while(true) { >> do some I/O (HDF5 POSIX output to a remote, parallel file system) >> wait for communication (MPI_Waitany) from other processes (in the same >> node and outside the node) >> } >> >> I'm measuring the energy consumption of the node that runs this process >> for the same duration, as a function of the amount of data written in each >> I/O operation. >> Surprisingly, the larger the I/O in proposition to the communication, the >> lower the energy consumption. In other words, the longer I wait in >> MPI_Waitany, the more I consume. >> >> Does anyone have a good explanation for that? Is there an active loop in >> MPI_Waitany? Another reason? >> >> Thanks! >> >> Matthieu >> > > > -- > Jeff Hammond > jeff.science(a)gmail.com > <javascript:_e(%7B%7D,'cvml','jeff.science(a)gmail.com');> > http://jeffhammond.github.io/ > -- Jeff Hammond jeff.science(a)gmail.com http://jeffhammond.github.io/ _______________________________________________ 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] Active loop in MPI_Waitany?
by Dorier, Matthieu 30 Jul '15

30 Jul '15

Not that obvious, a UNIX function like "select" would allow to block on a set of file descriptors (for instance sockets), so I was expecting MPI_Waitany to work kind of the same way. Pavan explained me (in person) why it does not: it cannot at the same time block on a read from shared memory (channels inside a node) and on network connections (outside the node). (I'm simplifying a bit here). So the answer is: yes, MPI_Waitany is actively looping. Matthieu ________________________________ From: Jeff Hammond [jeff.science(a)gmail.com] Sent: Thursday, July 30, 2015 6:41 PM To: discuss(a)mpich.org Subject: Re: [mpich-discuss] Active loop in MPI_Waitany? Seems obvious that Waitany spins on the array of requests until one completes. Is that an active loop by your definition? Jeff On Thursday, July 30, 2015, Dorier, Matthieu <mdorier(a)anl.gov<mailto:[email protected]>> wrote: Hi, I have a code that looks like this: while(true) { do some I/O (HDF5 POSIX output to a remote, parallel file system) wait for communication (MPI_Waitany) from other processes (in the same node and outside the node) } I'm measuring the energy consumption of the node that runs this process for the same duration, as a function of the amount of data written in each I/O operation. Surprisingly, the larger the I/O in proposition to the communication, the lower the energy consumption. In other words, the longer I wait in MPI_Waitany, the more I consume. Does anyone have a good explanation for that? Is there an active loop in MPI_Waitany? Another reason? Thanks! Matthieu -- Jeff Hammond jeff.science(a)gmail.com<mailto:[email protected]> http://jeffhammond.github.io/ _______________________________________________ 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] Active loop in MPI_Waitany?
by Jeff Hammond 30 Jul '15

30 Jul '15

Seems obvious that Waitany spins on the array of requests until one completes. Is that an active loop by your definition? Jeff On Thursday, July 30, 2015, Dorier, Matthieu <mdorier(a)anl.gov> wrote: > Hi, > > I have a code that looks like this: > > while(true) { > do some I/O (HDF5 POSIX output to a remote, parallel file system) > wait for communication (MPI_Waitany) from other processes (in the same > node and outside the node) > } > > I'm measuring the energy consumption of the node that runs this process > for the same duration, as a function of the amount of data written in each > I/O operation. > Surprisingly, the larger the I/O in proposition to the communication, the > lower the energy consumption. In other words, the longer I wait in > MPI_Waitany, the more I consume. > > Does anyone have a good explanation for that? Is there an active loop in > MPI_Waitany? Another reason? > > Thanks! > > Matthieu > -- Jeff Hammond jeff.science(a)gmail.com http://jeffhammond.github.io/ _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Active loop in MPI_Waitany?
by Dorier, Matthieu 30 Jul '15

30 Jul '15

Hi, I have a code that looks like this: while(true) { do some I/O (HDF5 POSIX output to a remote, parallel file system) wait for communication (MPI_Waitany) from other processes (in the same node and outside the node) } I'm measuring the energy consumption of the node that runs this process for the same duration, as a function of the amount of data written in each I/O operation. Surprisingly, the larger the I/O in proposition to the communication, the lower the energy consumption. In other words, the longer I wait in MPI_Waitany, the more I consume. Does anyone have a good explanation for that? Is there an active loop in MPI_Waitany? Another reason? Thanks! Matthieu _______________________________________________ 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] Nemesis engine
by Halim Amer 30 Jul '15

30 Jul '15

Hi Viswanath, Nemesis supports multithreading. Have you initialized the MPI environment with MPI_THREAD_MULTIPLE threading support? If you still see the problem after the above initialization, please send us a minimal example code that reproduces it. Thank you, --Halim Abdelhalim Amer (Halim) Postdoctoral Appointee MCS Division Argonne National Laboratory On 7/30/15 9:40 AM, Viswanath Krishnamurthy wrote: > Hi All, > > I am currently working on MPICH-version 3.1.4 on Ubuntu.. > where I get an error stating that > > Assertion failed in > file src/mpid/ch3/channels/nemesis/src/ch3_progress.c at Line 252 > * > * > The actual problem which I face is that currently even if MPI_Sends have > already been dispatched, certain nodes keep waiting for MPI_Recvs which > never arrive at all(Using multithreading). When I referred the internet, > my understanding is that nemesis is written to handle only one thread > receive. Please let me know about the latest patch for nemesis engine or > the mpich version which has the changes. > *src/mpid/ch3/channels/nemesis/src/ch3_progress.c * > > Thanks, > Viswanath > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] Nemesis engine
by Viswanath Krishnamurthy 30 Jul '15

30 Jul '15

Hi All, I am currently working on MPICH-version 3.1.4 on Ubuntu.. where I get an error stating that Assertion failed in file src/mpid/ch3/channels/nemesis/src/ch3_progress.c at Line 252 The actual problem which I face is that currently even if MPI_Sends have already been dispatched, certain nodes keep waiting for MPI_Recvs which never arrive at all(Using multithreading). When I referred the internet, my understanding is that nemesis is written to handle only one thread receive. Please let me know about the latest patch for nemesis engine or the mpich version which has the changes. *src/mpid/ch3/channels/nemesis/src/ch3_progress.c * Thanks, Viswanath _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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