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

Re: [mpich-discuss] MPI_Win_fence failed
by Sufeng Niu 10 Jul '13

10 Jul '13

Sorry I forget to add screen shot for backtrace. the screen shot is attached. Thanks a lot! Sufeng On Wed, Jul 10, 2013 at 11:30 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. Re: MPI_Win_fence failed (Sufeng Niu) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 10 Jul 2013 11:30:36 -0500 > From: Sufeng Niu <sniu(a)hawk.iit.edu> > To: discuss(a)mpich.org > Subject: Re: [mpich-discuss] MPI_Win_fence failed > Message-ID: > < > CAFNNHkyLj8CbYMmc_w2DA9_+q2Oe3kyus+g6c99ShPk6ZXVkdA(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Jim, > > Thanks a lot for your reply. the basic way for me to debugging is > barrier+printf, right now I only have an evaluation version of totalview. > the backtrace using totalview shown below. the udp is the udp collection > and create RMA window, image_rms doing MPI_Get to access the window > > There is a segment violation, but I don't know why the program stopped at > MPI_Win_fence. > > Thanks a lot! > > > > > > > > On Wed, Jul 10, 2013 at 10:12 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. Re: MPICH3.0.4 make fails with "No rule to make target..." > > (Wesley Bland) > > 2. Re: Error in MPI_Finalize on a simple ring test over TCP > > (Wesley Bland) > > 3. Restrict number of cores, not threads (Bob Ilgner) > > 4. Re: Restrict number of cores, not threads (Wesley Bland) > > 5. Re: Restrict number of cores, not threads (Wesley Bland) > > 6. Re: Error in MPI_Finalize on a simple ring test over TCP > > (Thomas Ropars) > > 7. MPI_Win_fence failed (Sufeng Niu) > > 8. Re: MPI_Win_fence failed (Jim Dinan) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Wed, 10 Jul 2013 08:29:06 -0500 > > From: Wesley Bland <wbland(a)mcs.anl.gov> > > To: discuss(a)mpich.org > > Subject: Re: [mpich-discuss] MPICH3.0.4 make fails with "No rule to > > make target..." > > Message-ID: <F48FC916-31F7-4F82-95F8-2D6A6C45264F(a)mcs.anl.gov> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Unfortunately, due to the lack of developer resources and interest, the > > last version of MPICH which was supported on Windows was 1.4.1p. You can > > find that version on the downloads page: > > > > http://www.mpich.org/downloads/ > > > > Alternatively, Microsoft maintains a derivative of MPICH which should > > provide the features you need. You also find a link to that on the > > downloads page above. > > > > Wesley > > > > On Jul 10, 2013, at 1:16 AM, Don Warren <don.warren(a)gmail.com> wrote: > > > > > Hello, > > > > > > As requested in the installation guide, I'm informing this list of a > > failure to correctly make MPICH3.0.4 on a Win7 system. The specific > error > > encountered is > > > "make[2]: *** No rule to make target > > `/cygdrive/c/FLASH/mpich-3.0.4/src/mpi/romio/Makefile.am', needed by > > `/cygdrive/c/FLASH/mpich-3.0.4/src/mpi/romio/Makefile.in'. Stop." > > > > > > I have confirmed that both Makefile.am and Makefile.in exist in the > > directory listed. I'm attaching the c.txt and the m.txt files. > > > > > > Possibly of interest is that the command "make clean" fails at exactly > > the same folder, with exactly the same error message as shown in m.txt > and > > above. > > > > > > Any advice you can give would be appreciated. I'm attempting to get > > FLASH running on my computer, which seems to require MPICH. > > > > > > Regards, > > > Don Warren > > > > <config-make-outputs.zip>_______________________________________________ > > > discuss mailing list discuss(a)mpich.org > > > To manage subscription options or unsubscribe: > > > https://lists.mpich.org/mailman/listinfo/discuss > > > >

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Re: [mpich-discuss] MPI_Win_fence failed
by Sufeng Niu 10 Jul '13

10 Jul '13

Hi Jim, Thanks a lot for your reply. the basic way for me to debugging is barrier+printf, right now I only have an evaluation version of totalview. the backtrace using totalview shown below. the udp is the udp collection and create RMA window, image_rms doing MPI_Get to access the window There is a segment violation, but I don't know why the program stopped at MPI_Win_fence. Thanks a lot! On Wed, Jul 10, 2013 at 10:12 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. Re: MPICH3.0.4 make fails with "No rule to make target..." > (Wesley Bland) > 2. Re: Error in MPI_Finalize on a simple ring test over TCP > (Wesley Bland) > 3. Restrict number of cores, not threads (Bob Ilgner) > 4. Re: Restrict number of cores, not threads (Wesley Bland) > 5. Re: Restrict number of cores, not threads (Wesley Bland) > 6. Re: Error in MPI_Finalize on a simple ring test over TCP > (Thomas Ropars) > 7. MPI_Win_fence failed (Sufeng Niu) > 8. Re: MPI_Win_fence failed (Jim Dinan) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 10 Jul 2013 08:29:06 -0500 > From: Wesley Bland <wbland(a)mcs.anl.gov> > To: discuss(a)mpich.org > Subject: Re: [mpich-discuss] MPICH3.0.4 make fails with "No rule to > make target..." > Message-ID: <F48FC916-31F7-4F82-95F8-2D6A6C45264F(a)mcs.anl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > Unfortunately, due to the lack of developer resources and interest, the > last version of MPICH which was supported on Windows was 1.4.1p. You can > find that version on the downloads page: > > http://www.mpich.org/downloads/ > > Alternatively, Microsoft maintains a derivative of MPICH which should > provide the features you need. You also find a link to that on the > downloads page above. > > Wesley > > On Jul 10, 2013, at 1:16 AM, Don Warren <don.warren(a)gmail.com> wrote: > > > Hello, > > > > As requested in the installation guide, I'm informing this list of a > failure to correctly make MPICH3.0.4 on a Win7 system. The specific error > encountered is > > "make[2]: *** No rule to make target > `/cygdrive/c/FLASH/mpich-3.0.4/src/mpi/romio/Makefile.am', needed by > `/cygdrive/c/FLASH/mpich-3.0.4/src/mpi/romio/Makefile.in'. Stop." > > > > I have confirmed that both Makefile.am and Makefile.in exist in the > directory listed. I'm attaching the c.txt and the m.txt files. > > > > Possibly of interest is that the command "make clean" fails at exactly > the same folder, with exactly the same error message as shown in m.txt and > above. > > > > Any advice you can give would be appreciated. I'm attempting to get > FLASH running on my computer, which seems to require MPICH. > > > > Regards, > > Don Warren > > <config-make-outputs.zip>_______________________________________________ > > discuss mailing list discuss(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > >

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Re: [mpich-discuss] MPI_Win_fence failed
by Jim Dinan 10 Jul '13

10 Jul '13

It's hard to tell where the segmentation fault is coming from. Can you use a debugger to generate a backtrace? ~Jim. On Wed, Jul 10, 2013 at 11:07 AM, Sufeng Niu <sniu(a)hawk.iit.edu> wrote: > Hello, > > I used MPI RMA in my program, but the program stop at the MPI_Win_fence, I > have a master process receive data from udp socket. Other processes use > MPI_Get to access data. > > master process: > > MPI_Create(...) > for(...){ > /* udp recv operation */ > > MPI_Barrier // to let other process know data received from udp is ready > > MPI_Win_fence(0, win); > MPI_Win_fence(0, win); > > } > > other processes: > > for(...){ > > MPI_Barrier // sync for udp data ready > > MPI_Win_fence(0, win); > > MPI_Get(); > > MPI_Win_fence(0, win); <-- program stopped here > > /* other operation */ > } > > I found that the program stopped at second MPI_Win_fence, the terminal > output is: > > > > =================================================================================== > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = EXIT CODE: 11 > = 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 > > Do you have any suggestions? Thank you very much! > > -- > Best Regards, > Sufeng Niu > ECASP lab, ECE department, Illinois Institute of Technology > Tel: 312-731-7219 > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss >

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MPI_Win_fence failed
by Sufeng Niu 10 Jul '13

10 Jul '13

Hello, I used MPI RMA in my program, but the program stop at the MPI_Win_fence, I have a master process receive data from udp socket. Other processes use MPI_Get to access data. master process: MPI_Create(...) for(...){ /* udp recv operation */ MPI_Barrier // to let other process know data received from udp is ready MPI_Win_fence(0, win); MPI_Win_fence(0, win); } other processes: for(...){ MPI_Barrier // sync for udp data ready MPI_Win_fence(0, win); MPI_Get(); MPI_Win_fence(0, win); <-- program stopped here /* other operation */ } I found that the program stopped at second MPI_Win_fence, the terminal output is: =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 11 = 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 Do you have any suggestions? Thank you very much! -- Best Regards, Sufeng Niu ECASP lab, ECE department, Illinois Institute of Technology Tel: 312-731-7219

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Re: [mpich-discuss] Error in MPI_Finalize on a simple ring test over TCP
by Thomas Ropars 10 Jul '13

10 Jul '13

Yes, you are right, sorry for disturbing. On 07/10/2013 03:39 PM, Wesley Bland wrote: > The value of previous for rank 0 in your code is -1. MPICH is complaining because all of the requests to receive a message from -1 are still pending when you try to finalize. You need to make sure that you are receiving from valid ranks. > > On Jul 10, 2013, at 7:50 AM, Thomas Ropars <thomas.ropars(a)epfl.ch> wrote: > >> Yes sure. Here it is. >> >> Thomas >> >> On 07/10/2013 02:23 PM, Wesley Bland wrote: >>> Can you send us the smallest chunk of code that still exhibits this error? >>> >>> Wesley >>> >>> On Jul 10, 2013, at 6:54 AM, Thomas Ropars <thomas.ropars(a)epfl.ch> wrote: >>> >>>> Hi all, >>>> >>>> I get the following error when I try to run a simple application implementing a ring (each process sends to rank+1 and receives from rank-1). More precisely, the error occurs during the call to MPI_Finalize(): >>>> >>>> Assertion failed in file src/mpid/ch3/channels/nemesis/netmod/tcp/socksm.c at line 363: sc->pg_is_set >>>> internal ABORT - process 0 >>>> >>>> Does anybody else also noticed the same error? >>>> >>>> Here are all the details about my test: >>>> - The error is generated with mpich-3.0.2 (but I noticed the exact same error with mpich-3.0.4) >>>> - I am using IPoIB for communication between nodes (The same thing happens over Ethernet) >>>> - The problem comes from TCP links. When all processes are on the same node, there is no error. As soon as one process is on a remote node, the failure occurs. >>>> - Note also that the failure does not occur if I run a more complex code (eg, a NAS benchmark). >>>> >>>> Thomas Ropars >>>> _______________________________________________ >>>> 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 >>> >>> >> <ring_clean.c>_______________________________________________ >> 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] Restrict number of cores, not threads
by Wesley Bland 10 Jul '13

10 Jul '13

Threads in MPI are not ranks. When you say you want to launch with -n 100, you will always get 100 processes, not threads. If you want 10 threads on 10 cores, you will need to launch with -n 10, then add your threads according to your threading library. Note that threads in MPI do not get their own rank currently. They all share the same rank as the process in which they reside, so if you need to be able to handle things with different ranks, you'll need to use actual processes. Wesley On Jul 10, 2013, at 9:41 AM, Bob Ilgner <bobilgner(a)gmail.com> wrote: > Dear all, > > I am working on a shared memory processor with 256 cores. I am working from the command line directly. > > Can I restict the number of cores that I deploy.The command > > mpirun -n 100 myprog > > > will automatically start on 100 cores. I wish to use only 10 cores and have 10 threads on each core. Can I do this with mpich ? Rememebre that this an smp abd I can not identify each core individually(as in a cluster) > > Regards, bob > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

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Restrict number of cores, not threads
by Bob Ilgner 10 Jul '13

10 Jul '13

Dear all, I am working on a shared memory processor with 256 cores. I am working from the command line directly. Can I restict the number of cores that I deploy.The command mpirun -n 100 myprog will automatically start on 100 cores. I wish to use only 10 cores and have 10 threads on each core. Can I do this with mpich ? Rememebre that this an smp abd I can not identify each core individually(as in a cluster) Regards, bob

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Re: [mpich-discuss] Error in MPI_Finalize on a simple ring test over TCP
by Wesley Bland 10 Jul '13

10 Jul '13

The value of previous for rank 0 in your code is -1. MPICH is complaining because all of the requests to receive a message from -1 are still pending when you try to finalize. You need to make sure that you are receiving from valid ranks. On Jul 10, 2013, at 7:50 AM, Thomas Ropars <thomas.ropars(a)epfl.ch> wrote: > Yes sure. Here it is. > > Thomas > > On 07/10/2013 02:23 PM, Wesley Bland wrote: >> Can you send us the smallest chunk of code that still exhibits this error? >> >> Wesley >> >> On Jul 10, 2013, at 6:54 AM, Thomas Ropars <thomas.ropars(a)epfl.ch> wrote: >> >>> Hi all, >>> >>> I get the following error when I try to run a simple application implementing a ring (each process sends to rank+1 and receives from rank-1). More precisely, the error occurs during the call to MPI_Finalize(): >>> >>> Assertion failed in file src/mpid/ch3/channels/nemesis/netmod/tcp/socksm.c at line 363: sc->pg_is_set >>> internal ABORT - process 0 >>> >>> Does anybody else also noticed the same error? >>> >>> Here are all the details about my test: >>> - The error is generated with mpich-3.0.2 (but I noticed the exact same error with mpich-3.0.4) >>> - I am using IPoIB for communication between nodes (The same thing happens over Ethernet) >>> - The problem comes from TCP links. When all processes are on the same node, there is no error. As soon as one process is on a remote node, the failure occurs. >>> - Note also that the failure does not occur if I run a more complex code (eg, a NAS benchmark). >>> >>> Thomas Ropars >>> _______________________________________________ >>> 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 >> >> > > <ring_clean.c>_______________________________________________ > 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] MPICH3.0.4 make fails with "No rule to make target..."
by Wesley Bland 10 Jul '13

10 Jul '13

Unfortunately, due to the lack of developer resources and interest, the last version of MPICH which was supported on Windows was 1.4.1p. You can find that version on the downloads page: http://www.mpich.org/downloads/ Alternatively, Microsoft maintains a derivative of MPICH which should provide the features you need. You also find a link to that on the downloads page above. Wesley On Jul 10, 2013, at 1:16 AM, Don Warren <don.warren(a)gmail.com> wrote: > Hello, > > As requested in the installation guide, I'm informing this list of a failure to correctly make MPICH3.0.4 on a Win7 system. The specific error encountered is > "make[2]: *** No rule to make target `/cygdrive/c/FLASH/mpich-3.0.4/src/mpi/romio/Makefile.am', needed by `/cygdrive/c/FLASH/mpich-3.0.4/src/mpi/romio/Makefile.in'. Stop." > > I have confirmed that both Makefile.am and Makefile.in exist in the directory listed. I'm attaching the c.txt and the m.txt files. > > Possibly of interest is that the command "make clean" fails at exactly the same folder, with exactly the same error message as shown in m.txt and above. > > Any advice you can give would be appreciated. I'm attempting to get FLASH running on my computer, which seems to require MPICH. > > Regards, > Don Warren > <config-make-outputs.zip>_______________________________________________ > 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 in MPI_Finalize on a simple ring test over TCP
by Thomas Ropars 10 Jul '13

10 Jul '13

Yes sure. Here it is. Thomas On 07/10/2013 02:23 PM, Wesley Bland wrote: > Can you send us the smallest chunk of code that still exhibits this error? > > Wesley > > On Jul 10, 2013, at 6:54 AM, Thomas Ropars <thomas.ropars(a)epfl.ch> wrote: > >> Hi all, >> >> I get the following error when I try to run a simple application implementing a ring (each process sends to rank+1 and receives from rank-1). More precisely, the error occurs during the call to MPI_Finalize(): >> >> Assertion failed in file src/mpid/ch3/channels/nemesis/netmod/tcp/socksm.c at line 363: sc->pg_is_set >> internal ABORT - process 0 >> >> Does anybody else also noticed the same error? >> >> Here are all the details about my test: >> - The error is generated with mpich-3.0.2 (but I noticed the exact same error with mpich-3.0.4) >> - I am using IPoIB for communication between nodes (The same thing happens over Ethernet) >> - The problem comes from TCP links. When all processes are on the same node, there is no error. As soon as one process is on a remote node, the failure occurs. >> - Note also that the failure does not occur if I run a more complex code (eg, a NAS benchmark). >> >> Thomas Ropars >> _______________________________________________ >> 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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