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

Re: [mpich-discuss] OS X VPNs and mpirun
by Pavan Balaji 30 Nov '13

30 Nov '13

There have been some fixes to this in the mpich-3.1.x series. Did you try the latest mpich-3.1rc2 release? — Pavan On Nov 30, 2013, at 1:54 PM, Gideon Simpson <gideon.simpson(a)gmail.com> wrote: > I just noticed this, but when I try to use mpirun with programs on my OS X machine, while logged into a work VPN, the MPI code just hangs. If I disconnect from my VPN, the problem disappears. Is there a simple fix for this? > > -gideon > > _______________________________________________ > 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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OS X VPNs and mpirun
by Gideon Simpson 30 Nov '13

30 Nov '13

I just noticed this, but when I try to use mpirun with programs on my OS X machine, while logged into a work VPN, the MPI code just hangs. If I disconnect from my VPN, the problem disappears. Is there a simple fix for this? -gideon

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Re: [mpich-discuss] MPI_Recv problem
by Soheil Hooshdaran 30 Nov '13

30 Nov '13

So what do I have to do now, sir? Especially regarding my Bcast()s a,d Recv()s On Sat, Nov 30, 2013 at 1:05 AM, Pavan Balaji <balaji(a)mcs.anl.gov> wrote: > > Please keep discuss(a)mpich.org cc’ed. > > On Nov 29, 2013, at 2:19 PM, Soheil Hooshdaran <shooshdaran577(a)gmail.com> > wrote: > > executing send for the 3th time > > executed send for the 3th time, sending 40 bytes > > Fatal error in MPI_Recv: Message truncated, error stack: > > MPI_Recv(184).....................: MPI_Recv(buf=0xbff95c98, count=0, > MPI_INT, src=0, tag=1, MPI_COMM_WORLD, status=0xbff95c70) failed > > MPIDI_CH3U_Receive_data_found(131): Message from rank 0 and tag 1 > truncated; 160 bytes received but buffer size is 0 > > I don’t think I can explain the error any better than what the message > above already says. > > -- > Pavan Balaji > http://www.mcs.anl.gov/~balaji >

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Re: [mpich-discuss] reading from a read only directory
by Jed Brown 30 Nov '13

30 Nov '13

Geoffrey Irving <irving(a)naml.us> writes: > It's not an issue for me personally anymore: chmod +w . is fine, and > symlinks would also solve the problem. The question was more about > the motivation for the code and whether it's an issue anything thinks > is worth fixing (or fixable at all). That and Jed asked me several > times to start the thread. :) It's not intuitive and does not appear to be documented. Reading from a read-only directory is a reasonable thing to try and people should not have to wait through a queue to find out that it doesn't work.

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Re: [mpich-discuss] reading from a read only directory
by Geoffrey Irving 29 Nov '13

29 Nov '13

On Fri, Nov 29, 2013 at 8:35 PM, Jeff Hammond <jeff.science(a)gmail.com> wrote: > Personally, I'd address the paranoia by saving a copy of your files > into a read-only directory. Since I know where you're running, I can > say that we should be able to afford the extra storage. If not, let > me know and I'll address it. And note also that NERSC $SCRATCH is not > backed up, so the safe place to story anything valuable is $HOME. I'm > not sure about project directories but I imagine there are docs on > this. > > It would be nice if it were possible to do read-only MPI-IO in a > read-only directory. I don't have a clue what the technical > challenges are. Can you not make just the files read-only but let new > files be created in the directory? It's not an issue for me personally anymore: chmod +w . is fine, and symlinks would also solve the problem. The question was more about the motivation for the code and whether it's an issue anything thinks is worth fixing (or fixable at all). That and Jed asked me several times to start the thread. :) Geoffrey

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Re: [mpich-discuss] reading from a read only directory
by Jeff Hammond 29 Nov '13

29 Nov '13

Personally, I'd address the paranoia by saving a copy of your files into a read-only directory. Since I know where you're running, I can say that we should be able to afford the extra storage. If not, let me know and I'll address it. And note also that NERSC $SCRATCH is not backed up, so the safe place to story anything valuable is $HOME. I'm not sure about project directories but I imagine there are docs on this. It would be nice if it were possible to do read-only MPI-IO in a read-only directory. I don't have a clue what the technical challenges are. Can you not make just the files read-only but let new files be created in the directory? Jeff On Wed, Nov 27, 2013 at 11:32 PM, Geoffrey Irving <irving(a)naml.us> wrote: > I got the following error trying to slurp in a large file > (slice-17.pentago) with MPI_File_read_ordered: > > rank 0: pentago/mpi/io.cpp:read_sections:397: > MPI_File_read_ordered(file,raw.data(),raw.size(),MPI_BYTE,MPI_STATUS_IGNO > ADIOI_CRAY_OPEN(102): Access denied to file all-1/.slice-17.pentago.shfp.670064 > > The directory all-1 was read only due to paranoia over accidentally > deleting expensively obtained data. Looking at ADIOI_Shfp_fname in > the mpich source, it looks like this error is intentional: the shared > file pointer routines generate temporary files in the same directory > as the read-from file. I couldn't find any attempts at recovery if > the file cannot be written in that place. This behavior doesn't seem > to have changed since the beginning of the git repository. > > Is my reading of the code correct: MPI_File_read_ordered can't be used > on a file in a read only directory? > > I can see the motivation for this in the case of noncollective shared > routines: since the other processes aren't necessarily doing any MPI > at the moment, the only way to synchronize is through the file system. > And because there might be all sorts of different filesystems in > operation, the easiest way to ensure that we're touching the right one > is use the same directory. I can't imagine any reasonable use of the > noncollective shared routines, but maybe that's a different > discussion. Is this an unfortunate leak between broken routines which > need questionable trickery and perfectly good routines like > MPI_File_read_ordered? > > Thanks, > Geoffrey > _______________________________________________ > 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

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Re: [mpich-discuss] MPI_Recv problem
by Pavan Balaji 29 Nov '13

29 Nov '13

Please keep discuss(a)mpich.org cc’ed. On Nov 29, 2013, at 2:19 PM, Soheil Hooshdaran <shooshdaran577(a)gmail.com> wrote: > executing send for the 3th time > executed send for the 3th time, sending 40 bytes > Fatal error in MPI_Recv: Message truncated, error stack: > MPI_Recv(184).....................: MPI_Recv(buf=0xbff95c98, count=0, MPI_INT, src=0, tag=1, MPI_COMM_WORLD, status=0xbff95c70) failed > MPIDI_CH3U_Receive_data_found(131): Message from rank 0 and tag 1 truncated; 160 bytes received but buffer size is 0 I don’t think I can explain the error any better than what the message above already says. -- Pavan Balaji http://www.mcs.anl.gov/~balaji

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Re: [mpich-discuss] MPI_Recv problem
by Pavan Balaji 29 Nov '13

29 Nov '13

Please don’t rely on stdin. Read from a file if you like or pass the input parameters as command-line arguments. In your Bcast operation, you are sending a bunch of pointers, and not the actual array. Can you create *one* simple program that reproduces the error and send it to us? — Pavan On Nov 29, 2013, at 1:18 PM, Soheil Hooshdaran <shooshdaran577(a)gmail.com> wrote: > One of these two caused the error > > > On Fri, Nov 29, 2013 at 10:29 PM, Pavan Balaji <balaji(a)mcs.anl.gov> wrote: > > Please keep discuss(a)mpich.org cc’ed. > > Do you have a simple program that demonstrates this error? > > — Pavan > > On Nov 29, 2013, at 12:50 PM, Soheil Hooshdaran <shooshdaran577(a)gmail.com> wrote: > > > Dear sir > > Hi. > > Do you need My source code to judge my error? > > I am running Ubuntu 12.04 LTS and get > > MPI_Recv(184).....................: MPI_Recv(buf=0xbfd571e8, count=0, > > MPI_INT, src=0, tag=1, MPI_COMM_WORLD, status=0xbfd571c0) failed > > as I have already told you through discuss(a)mpich.org > > -- > Pavan Balaji > http://www.mcs.anl.gov/~balaji > > > <p1_Hooshdaran_static[debug].cpp><p1_Hooshdaran_static[debug1D].cpp> -- Pavan Balaji http://www.mcs.anl.gov/~balaji

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Re: [mpich-discuss] MPI_Recv problem
by Soheil Hooshdaran 29 Nov '13

29 Nov '13

One of these two caused the error On Fri, Nov 29, 2013 at 10:29 PM, Pavan Balaji <balaji(a)mcs.anl.gov> wrote: > > Please keep discuss(a)mpich.org cc’ed. > > Do you have a simple program that demonstrates this error? > > — Pavan > > On Nov 29, 2013, at 12:50 PM, Soheil Hooshdaran <shooshdaran577(a)gmail.com> > wrote: > > > Dear sir > > Hi. > > Do you need My source code to judge my error? > > I am running Ubuntu 12.04 LTS and get > > MPI_Recv(184).....................: MPI_Recv(buf=0xbfd571e8, count=0, > > MPI_INT, src=0, tag=1, MPI_COMM_WORLD, status=0xbfd571c0) failed > > as I have already told you through discuss(a)mpich.org > > -- > Pavan Balaji > http://www.mcs.anl.gov/~balaji > >

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Re: [mpich-discuss] MPI_Recv problem
by Pavan Balaji 29 Nov '13

29 Nov '13

Please keep discuss(a)mpich.org cc’ed. Do you have a simple program that demonstrates this error? — Pavan On Nov 29, 2013, at 12:50 PM, Soheil Hooshdaran <shooshdaran577(a)gmail.com> wrote: > Dear sir > Hi. > Do you need My source code to judge my error? > I am running Ubuntu 12.04 LTS and get > MPI_Recv(184).....................: MPI_Recv(buf=0xbfd571e8, count=0, > MPI_INT, src=0, tag=1, MPI_COMM_WORLD, status=0xbfd571c0) failed > as I have already told you through discuss(a)mpich.org -- Pavan Balaji http://www.mcs.anl.gov/~balaji

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