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

Re: [mpich-discuss] Use other's mpicc to compile code with my modified ROMIO
by Jaln 05 Oct '14

05 Oct '14

Hi Rob, Thanks, I’m adding some experimental features in ROMIO, ROMIO can be built as a standalone library. If you link it on top of your mpi program, it will override the existing MPI-IO calls. Can you please tell me how to compile the code with a standalone ROMIO? For example, with cray’s default mpi compiler, and a modified ROMIO source, and a test MPI program, e.g., test.c I saw one old post in mpich-discuss, ‘building external ROMIO’, I believe that guy was asking the similar questions, but I think I didn’t get the answers from that post. Thanks Rob, Best, Jialin On Sun, Oct 5, 2014 at 4:00 PM, Rob Latham <robl(a)mcs.anl.gov> wrote: > > > On 10/04/2014 08:57 PM, Jaln wrote: > > I have a modified ROMIO library, >> > > Hello! I would love to hear more about the modifications you are exploring > in ROMIO. > > > but I have to compile the code using > >> NERSC Hopper's default MPI compiler, is there any way to let the >> collective I/O code run with my modified ROMIO library. (and of course >> compile using their default mpicc) >> > > ROMIO can be built as a standalone library. If you link it on top of your > mpi program, it will override the existing MPI-IO calls. > > I try to compile my own mpicc and run on that cluster, but seems, the >> hopper cluster >> has specific optimized cray-mpi compiler and wont let my code compiled >> or executed correctly on compute nodes. >> > > I'm sure it's possible to do whatever the cray-mpi compiler is doing, but > Wei-keng Liao at Northwestern has done the standalone external library > approach on past cray machines -- including Hopper, I think. > > ==rob > -- > Rob Latham > Mathematics and Computer Science Division > Argonne National Lab, IL USA > _______________________________________________ > 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] Use other's mpicc to compile code with my modified ROMIO
by Rob Latham 05 Oct '14

05 Oct '14

On 10/04/2014 08:57 PM, Jaln wrote: > I have a modified ROMIO library, Hello! I would love to hear more about the modifications you are exploring in ROMIO. > but I have to compile the code using > NERSC Hopper's default MPI compiler, is there any way to let the > collective I/O code run with my modified ROMIO library. (and of course > compile using their default mpicc) ROMIO can be built as a standalone library. If you link it on top of your mpi program, it will override the existing MPI-IO calls. > I try to compile my own mpicc and run on that cluster, but seems, the > hopper cluster > has specific optimized cray-mpi compiler and wont let my code compiled > or executed correctly on compute nodes. I'm sure it's possible to do whatever the cray-mpi compiler is doing, but Wei-keng Liao at Northwestern has done the standalone external library approach on past cray machines -- including Hopper, I think. ==rob -- Rob Latham Mathematics and Computer Science Division Argonne National Lab, IL USA _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Use other's mpicc to compile code with my modified ROMIO
by Jaln 04 Oct '14

04 Oct '14

Hi, I have a modified ROMIO library, but I have to compile the code using NERSC Hopper's default MPI compiler, is there any way to let the collective I/O code run with my modified ROMIO library. (and of course compile using their default mpicc) I try to compile my own mpicc and run on that cluster, but seems, the hopper cluster has specific optimized cray-mpi compiler and wont let my code compiled or executed correctly on compute nodes. Thanks, Jialin _______________________________________________ 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: failed to allocate memory for an unexpected message
by XingFENG 03 Oct '14

03 Oct '14

Hi Wesley Bland, When I was searching on the Internet, I realized that it could because the mpich installed on these machines are too old. I found a FAQ entry as below : https://wiki.mpich.org/mpich/index.php/Frequently_Asked_Questions#Q:_I_don.… I installed an up-to-date version of OpenMPI on these two machines. And the problem is gone. I guess a recent MPICH would help, too. Thanks very much for your time. On Thu, Oct 2, 2014 at 8:57 PM, XingFENG <xingfeng(a)cse.unsw.edu.au> wrote: > Hi Wesley Bland, > > Thanks for your reply. > > My codes is relatively big( around 2000 lines). I will try to make and > post one small example later. > > On Thu, Oct 2, 2014 at 8:50 PM, Wesley Bland <wbland(a)anl.gov> wrote: > >> Can you provide a minimal example code that reproduced the problem? >> >> >> >> On Oct 2, 2014, at 2:13 AM, XingFENG <xingfeng(a)cse.unsw.edu.au> wrote: >> >> Hi Wesley Bland, >> >> Thanks for your reply. >> >> I have modified my codes. For each process, it first receives then sends >> message from/to others. However, same error still appears. >> >> I also noted that the code works fine for single node machine. It crushed >> with this error on multi-node cluster. >> >> >> On Sun, Sep 28, 2014 at 10:44 PM, Wesley Bland <wbland(a)anl.gov> wrote: >> >>> The problem in this situation usually is that you're not posting enough >>> receives and too many of your messages are getting buffered by the MPI >>> library. Make sure you match up your sends and receives and whenever >>> possible you post your receives early. >>> >>> Wesley >>> >>> >>> >>> > On Sep 28, 2014, at 7:13 AM, XingFENG <xingfeng(a)cse.unsw.edu.au> >>> wrote: >>> > >>> > Hi all, >>> > >>> > I am running a MPI program on two machines. I got errors as follows: >>> > >>> > >>> > ==================================================================== >>> > Fatal error in MPI_Test: Other MPI error, error stack: >>> > MPI_Test(153)......................: MPI_Test(request=0xa0a088, >>> flag=0x7fff470e86fc, status=0x7fff470e86e0) failed >>> > MPIDI_CH3I_Progress(150)...........: >>> > MPID_nem_mpich2_test_recv(800).....: >>> > MPID_nem_tcp_connpoll(1720)........: >>> > state_commrdy_handler(1556)........: >>> > MPID_nem_tcp_recv_handler(1459)....: >>> > MPID_nem_handle_pkt(493)...........: >>> > MPIDI_CH3_PktHandler_EagerSend(589): Failed to allocate memory for an >>> unexpected message. 261892 unexpected messages queued. >>> > Fatal error in MPI_Test: Other MPI error, error stack: >>> > MPI_Test(153)......................: MPI_Test(request=0xadb128, >>> flag=0x7fff33cba448, status=0x7fff33cba430) failed >>> > MPIDI_CH3I_Progress(150)...........: >>> > MPID_nem_mpich2_test_recv(800).....: >>> > MPID_nem_tcp_connpoll(1720)........: >>> > state_commrdy_handler(1556)........: >>> > MPID_nem_tcp_recv_handler(1459)....: >>> > MPID_nem_handle_pkt(493)...........: >>> > MPIDI_CH3_PktHandler_EagerSend(589): Failed to allocate memory for an >>> unexpected message. 261890 unexpected messages queued. >>> > rank 1 in job 11 slave_36134 caused collective abort of all ranks >>> > exit status of rank 1: killed by signal 9 >>> > >>> > ==================================================================== >>> > >>> > >>> > I have never seen such errors before. What is the cause of this error? >>> Is it an out of memory error? ( There is 20% remaining memory on machines ) >>> > >>> > Any help would be greatly appreciated. Thanks in advance! >>> > >>> > >>> > -- >>> > Best Regards. >>> > --- >>> > Xing FENG >>> > PhD Candidate >>> > Database Research Group >>> > >>> > School of Computer Science and Engineering >>> > University of New South Wales >>> > NSW 2052, Sydney >>> > >>> > Phone: (+61) 413 857 288 >>> > _______________________________________________ >>> > 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 >>> >> >> >> >> -- >> Best Regards. >> --- >> Xing FENG >> PhD Candidate >> Database Research Group >> >> School of Computer Science and Engineering >> University of New South Wales >> NSW 2052, Sydney >> >> Phone: (+61) 413 857 288 >> >> _______________________________________________ >> 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 >> > > > > -- > Best Regards. > --- > Xing FENG > PhD Candidate > Database Research Group > > School of Computer Science and Engineering > University of New South Wales > NSW 2052, Sydney > > Phone: (+61) 413 857 288 > -- Best Regards. --- Xing FENG PhD Candidate Database Research Group School of Computer Science and Engineering University of New South Wales NSW 2052, Sydney Phone: (+61) 413 857 288 _______________________________________________ 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] Issues installing MPICH on Ubuntu 14.04
by Kenneth Raffenetti 02 Oct '14

02 Oct '14

You need to make sure /Home/Mike/mpich-3.1.2-install/bin is in your PATH. That looks to be the actual install location. On 10/02/2014 01:08 PM, mhgardner wrote: > It seems like the install went through fine, but when I check which > mpicc and which mpiexec nothing happens. Do I need to use apt-get to get > these going or did something else go wrong? > > Appreciate the help! > > On Thu, Oct 2, 2014 at 10:44 AM, mhgardner <mhgardner(a)berkeley.edu > <mailto:[email protected]>> wrote: > > Great, thank you very much. > > On Thu, Oct 2, 2014 at 10:38 AM, Wesley Bland <wbland(a)anl.gov > <mailto:[email protected]>> wrote: > > From your config.log, it looks like you don’t have a Fortran > compiler installed. If you don’t plan to use it, that’s fine, > but you should pass —disable-fortran to the configure script. > > Thanks, > Wesley > >> On Oct 2, 2014, at 12:35 PM, mhgardner <mhgardner(a)berkeley.edu >> <mailto:[email protected]>> wrote: >> >> Hi, >> >> I'm trying to install MPICH in Ubuntu 14.04, but when I try to >> build it says no targets are specified. I'm following the >> install instructions from the following page: >> http://www.mpich.org/static/downloads/3.1.2/mpich-3.1.2-installguide.pdf >> The c.txt and m.txt files are attached. >> Not sure where things are going wrong, so any guidance would >> great. >> >> Thanks, >> >> Mike >> <c.txt><m.txt>_______________________________________________ >> discuss mailing list discuss(a)mpich.org <mailto:[email protected]> >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > 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 > _______________________________________________ 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] Issues installing MPICH on Ubuntu 14.04
by mhgardner 02 Oct '14

02 Oct '14

It seems like the install went through fine, but when I check which mpicc and which mpiexec nothing happens. Do I need to use apt-get to get these going or did something else go wrong? Appreciate the help! On Thu, Oct 2, 2014 at 10:44 AM, mhgardner <mhgardner(a)berkeley.edu> wrote: > Great, thank you very much. > > On Thu, Oct 2, 2014 at 10:38 AM, Wesley Bland <wbland(a)anl.gov> wrote: > >> From your config.log, it looks like you don’t have a Fortran compiler >> installed. If you don’t plan to use it, that’s fine, but you should pass >> —disable-fortran to the configure script. >> >> Thanks, >> Wesley >> >> On Oct 2, 2014, at 12:35 PM, mhgardner <mhgardner(a)berkeley.edu> wrote: >> >> Hi, >> >> I'm trying to install MPICH in Ubuntu 14.04, but when I try to build it >> says no targets are specified. I'm following the install instructions from >> the following page: >> http://www.mpich.org/static/downloads/3.1.2/mpich-3.1.2-installguide.pdf >> The c.txt and m.txt files are attached. >> Not sure where things are going wrong, so any guidance would great. >> >> Thanks, >> >> Mike >> <c.txt><m.txt>_______________________________________________ >> 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 >> > > _______________________________________________ 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] Issues installing MPICH on Ubuntu 14.04
by mhgardner 02 Oct '14

02 Oct '14

Great, thank you very much. On Thu, Oct 2, 2014 at 10:38 AM, Wesley Bland <wbland(a)anl.gov> wrote: > From your config.log, it looks like you don’t have a Fortran compiler > installed. If you don’t plan to use it, that’s fine, but you should pass > —disable-fortran to the configure script. > > Thanks, > Wesley > > On Oct 2, 2014, at 12:35 PM, mhgardner <mhgardner(a)berkeley.edu> wrote: > > Hi, > > I'm trying to install MPICH in Ubuntu 14.04, but when I try to build it > says no targets are specified. I'm following the install instructions from > the following page: > http://www.mpich.org/static/downloads/3.1.2/mpich-3.1.2-installguide.pdf > The c.txt and m.txt files are attached. > Not sure where things are going wrong, so any guidance would great. > > Thanks, > > Mike > <c.txt><m.txt>_______________________________________________ > 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 > _______________________________________________ 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] Issues installing MPICH on Ubuntu 14.04
by Rajeev Thakur 02 Oct '14

02 Oct '14

If you don't plan to use Fortran, just configure with --disable-fortran. Rajeev On Oct 2, 2014, at 12:35 PM, mhgardner <mhgardner(a)berkeley.edu> wrote: > Hi, > > I'm trying to install MPICH in Ubuntu 14.04, but when I try to build it says no targets are specified. I'm following the install instructions from the following page: http://www.mpich.org/static/downloads/3.1.2/mpich-3.1.2-installguide.pdf > The c.txt and m.txt files are attached. > Not sure where things are going wrong, so any guidance would great. > > Thanks, > > Mike > <c.txt><m.txt>_______________________________________________ > 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] Issues installing MPICH on Ubuntu 14.04
by Wesley Bland 02 Oct '14

02 Oct '14

From your config.log, it looks like you don’t have a Fortran compiler installed. If you don’t plan to use it, that’s fine, but you should pass —disable-fortran to the configure script. Thanks, Wesley > On Oct 2, 2014, at 12:35 PM, mhgardner <mhgardner(a)berkeley.edu> wrote: > > Hi, > > I'm trying to install MPICH in Ubuntu 14.04, but when I try to build it says no targets are specified. I'm following the install instructions from the following page: http://www.mpich.org/static/downloads/3.1.2/mpich-3.1.2-installguide.pdf <http://www.mpich.org/static/downloads/3.1.2/mpich-3.1.2-installguide.pdf> > The c.txt and m.txt files are attached. > Not sure where things are going wrong, so any guidance would great. > > Thanks, > > Mike > <c.txt><m.txt>_______________________________________________ > 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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Issues installing MPICH on Ubuntu 14.04
by mhgardner 02 Oct '14

02 Oct '14

Hi, I'm trying to install MPICH in Ubuntu 14.04, but when I try to build it says no targets are specified. I'm following the install instructions from the following page: http://www.mpich.org/static/downloads/3.1.2/mpich-3.1.2-installguide.pdf The c.txt and m.txt files are attached. Not sure where things are going wrong, so any guidance would great. Thanks, Mike

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