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

Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem
by Lee, Eibhlin 14 Jun '13

14 Jun '13

Gus, I tried running cpi, as is included in the installation of MPI, on two machines with two processes. The output message confirmed that it had started only 1 process instead of 2. Process 0 of 1 is on raspi pi is approximately... Then it just hung. I think this is because the other machine didn't know where to output the data? When I tried running two processes on the one machine using the wrapper you suggested the output was the same but doubled. It didn't hang. This confirms that every process was started with rank 0. I'm not entirely sure why /dev/mem is needed. I'm working in a group and another member set up io and gpio and it seemed it needed access to /dev/mem I am going to do a strace as suggested by Pavan Balaji to see where it is used and see if I can somehow work around it. Thank you for your help. Eibhlin ________________________________________ From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf of Gus Correa [gus(a)ldeo.columbia.edu] Sent: 13 June 2013 21:11 To: Discuss Mpich Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem Hi Eibhlin On 06/13/2013 12:59 PM, Lee, Eibhlin wrote: > Gus, > I believe your first assumption is correct. Unfortunately it just seemed to hang. I think this might be because each one is being made to have the same rank... Darn! I was afraid that it might give only rank 0 to all MPI processes. So, with the script wrapper the process being launched by mpiexec may indeed be sudo, not the actual mpi executable (main) :( Then it may actually launch a bunch of separate rank 0 replicas of your program, instead of assigning to them different ranks. However, without any output or error message, it is hard to tell. No output at all? No error message, just hangs? Have you tried a verbose flag (-v) to mpiexec? (Not sure if it exists in MPICH mpiexec, you'd need to check.) Would you care to try it with another mpi program, one that doesn't deal with /dev/mem (a risky business), say cpi.c (in the examples directory), or an mpi version of Hello, world, just to see if the mpiexec+sudo_script_wrapper works as expected or if everybody gets rank 0? > It may already be obvious but this is the first time I am using Linux. I had tried sudo $(which mpiexec ....) and sudo $(which mpiexec) ... both without success. "which mpiexec" will return the path to mpiexec, but won't execute it. You could try this (with backquotes): `which mpiexec` -n 2 ~/main On a side note, make sure the mpiexec you're using matches the mpicc/mpif90/MPI library from the MPICH that you used to compile the program. Often times computers have several flavors of MPI installed, and mixing them just doesn't work. > Is putting the full path to it similar to/is a symlink? (This still doesn't make main have super user privileges though.) No, nothing to do with sudo privileges. This suggestion was just to avoid messing up your /usr/bin, which is a directory that despite the somewhat misleading name (/usr, for historical reasons I think), is supposed to hold system (Linux) programs (that users can use), but not user-installed programs. Normally things are that are installed in /usr get there via some Linux package manager program (yum, rpm, apt-get, etc), to keep consistency with libraries, etc. I belive MPICH would install by default in /usr/local/ (and put mpiexec in /usr/local/bin), which is kind of a default location for non-system applications. The full path suggestion would be something like: /path/to/where/you/installed/mpiexec -n 2 ~/main However, this won't solve the other problem w.r.t. sudo and /dev/mem. You must know what you are doing, but it made me wonder, even if your program were sequential, why would you want to mess with /dev/mem directly? Just curious about it. Gus Correa > Eibhlin > ________________________________________ > From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf of Gus Correa [gus(a)ldeo.columbia.edu] > Sent: 13 June 2013 15:37 > To: Discuss Mpich > Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem > > Hi Lee > > How about replacing "~/main" in the mpiexec command line > by one-liner script? > Say, "sudo_main.sh", something like this: > > #! /bin/bash > sudo ~/main > > After all, it is "main" that accesses /dev/mem, > and needs "sudo" permissions, not mpiexec, right? > [Or do the mpiexec-launched processes inherit > the "sudo" stuff from mpiexec?] > > Not related, but, instead of putting mpiexec in /usr/bin, > can't you just use the full path to it? > > I hope this helps, > Gus Correa > > On 06/13/2013 10:09 AM, Lee, Eibhlin wrote: >> Pavan, >> I had a lot of trouble getting hydra to work without having to enter a password/passphrase. I saw the option to pass a phrase in the mpich installers guide. I eventually found that for that command you needed to use the smpd process manager. That's the only reason I chose smpd over hydra. >> As to your other suggestion. I ran ./main and the same error (Can't open /dev/mem...) appeared. sudo ./main works but of course without multiple processes. >> Eibhlin >> ________________________________________ >> From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf of Pavan Balaji [balaji(a)mcs.anl.gov] >> Sent: 13 June 2013 14:34 >> To: discuss(a)mpich.org >> Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem >> >> I just saw your older email. Why are you using smpd instead of the >> default process manager (hydra)? >> >> -- Pavan >> >> On 06/13/2013 08:05 AM, Pavan Balaji wrote: >>> What's "-phrase"? That's not a recognized option. I'm not sure where >>> the /dev/mem check is coming from. Try running ~/main without mpiexec >>> first. >>> >>> -- Pavan >>> >>> On 06/13/2013 06:56 AM, Lee, Eibhlin wrote: >>>> Hello all, >>>> >>>> I am trying to use two raspberry-pi to sample and then process some >>>> data. The first process samples while the second processes and vice >>>> versa. To do this I use gpio and also mpich-3.0.4 with the process >>>> manager smpd. I have successfully run cpi on both machines (from the >>>> master machine). I have also managed to run a similar program but >>>> without the MPI, this involved compiling with gcc and when running >>>> putting sudo in front of the binary file. >>>> >>>> When I combine these two processes I get various error messages. >>>> For input: >>>> mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>>> the error is: >>>> Can't open /dev/mem >>>> Did you forget to use 'sudo .. ?' >>>> >>>> For input: >>>> sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>>> the error is: >>>> sudo: mpiexec: Command not found >>>> >>>> I therefore put mpiexec into /usr/bin >>>> >>>> now for input: >>>> sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>>> the error is: >>>> Can't open /dev/mem >>>> Did you forget to use 'sudo .. ?' >>>> >>>> Does anyone know how I can work around this? >>>> Thanks, >>>> Eibhlin >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >> _______________________________________________ >> 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 > _______________________________________________ > 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] Running an mpi program that needs to access /dev/mem
by Gus Correa 13 Jun '13

13 Jun '13

Hi Eibhlin On 06/13/2013 12:59 PM, Lee, Eibhlin wrote: > Gus, > I believe your first assumption is correct. Unfortunately it just seemed to hang. I think this might be because each one is being made to have the same rank... Darn! I was afraid that it might give only rank 0 to all MPI processes. So, with the script wrapper the process being launched by mpiexec may indeed be sudo, not the actual mpi executable (main) :( Then it may actually launch a bunch of separate rank 0 replicas of your program, instead of assigning to them different ranks. However, without any output or error message, it is hard to tell. No output at all? No error message, just hangs? Have you tried a verbose flag (-v) to mpiexec? (Not sure if it exists in MPICH mpiexec, you'd need to check.) Would you care to try it with another mpi program, one that doesn't deal with /dev/mem (a risky business), say cpi.c (in the examples directory), or an mpi version of Hello, world, just to see if the mpiexec+sudo_script_wrapper works as expected or if everybody gets rank 0? > It may already be obvious but this is the first time I am using Linux. I had tried sudo $(which mpiexec ....) and sudo $(which mpiexec) ... both without success. "which mpiexec" will return the path to mpiexec, but won't execute it. You could try this (with backquotes): `which mpiexec` -n 2 ~/main On a side note, make sure the mpiexec you're using matches the mpicc/mpif90/MPI library from the MPICH that you used to compile the program. Often times computers have several flavors of MPI installed, and mixing them just doesn't work. > Is putting the full path to it similar to/is a symlink? (This still doesn't make main have super user privileges though.) No, nothing to do with sudo privileges. This suggestion was just to avoid messing up your /usr/bin, which is a directory that despite the somewhat misleading name (/usr, for historical reasons I think), is supposed to hold system (Linux) programs (that users can use), but not user-installed programs. Normally things are that are installed in /usr get there via some Linux package manager program (yum, rpm, apt-get, etc), to keep consistency with libraries, etc. I belive MPICH would install by default in /usr/local/ (and put mpiexec in /usr/local/bin), which is kind of a default location for non-system applications. The full path suggestion would be something like: /path/to/where/you/installed/mpiexec -n 2 ~/main However, this won't solve the other problem w.r.t. sudo and /dev/mem. You must know what you are doing, but it made me wonder, even if your program were sequential, why would you want to mess with /dev/mem directly? Just curious about it. Gus Correa > Eibhlin > ________________________________________ > From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf of Gus Correa [gus(a)ldeo.columbia.edu] > Sent: 13 June 2013 15:37 > To: Discuss Mpich > Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem > > Hi Lee > > How about replacing "~/main" in the mpiexec command line > by one-liner script? > Say, "sudo_main.sh", something like this: > > #! /bin/bash > sudo ~/main > > After all, it is "main" that accesses /dev/mem, > and needs "sudo" permissions, not mpiexec, right? > [Or do the mpiexec-launched processes inherit > the "sudo" stuff from mpiexec?] > > Not related, but, instead of putting mpiexec in /usr/bin, > can't you just use the full path to it? > > I hope this helps, > Gus Correa > > On 06/13/2013 10:09 AM, Lee, Eibhlin wrote: >> Pavan, >> I had a lot of trouble getting hydra to work without having to enter a password/passphrase. I saw the option to pass a phrase in the mpich installers guide. I eventually found that for that command you needed to use the smpd process manager. That's the only reason I chose smpd over hydra. >> As to your other suggestion. I ran ./main and the same error (Can't open /dev/mem...) appeared. sudo ./main works but of course without multiple processes. >> Eibhlin >> ________________________________________ >> From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf of Pavan Balaji [balaji(a)mcs.anl.gov] >> Sent: 13 June 2013 14:34 >> To: discuss(a)mpich.org >> Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem >> >> I just saw your older email. Why are you using smpd instead of the >> default process manager (hydra)? >> >> -- Pavan >> >> On 06/13/2013 08:05 AM, Pavan Balaji wrote: >>> What's "-phrase"? That's not a recognized option. I'm not sure where >>> the /dev/mem check is coming from. Try running ~/main without mpiexec >>> first. >>> >>> -- Pavan >>> >>> On 06/13/2013 06:56 AM, Lee, Eibhlin wrote: >>>> Hello all, >>>> >>>> I am trying to use two raspberry-pi to sample and then process some >>>> data. The first process samples while the second processes and vice >>>> versa. To do this I use gpio and also mpich-3.0.4 with the process >>>> manager smpd. I have successfully run cpi on both machines (from the >>>> master machine). I have also managed to run a similar program but >>>> without the MPI, this involved compiling with gcc and when running >>>> putting sudo in front of the binary file. >>>> >>>> When I combine these two processes I get various error messages. >>>> For input: >>>> mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>>> the error is: >>>> Can't open /dev/mem >>>> Did you forget to use 'sudo .. ?' >>>> >>>> For input: >>>> sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>>> the error is: >>>> sudo: mpiexec: Command not found >>>> >>>> I therefore put mpiexec into /usr/bin >>>> >>>> now for input: >>>> sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>>> the error is: >>>> Can't open /dev/mem >>>> Did you forget to use 'sudo .. ?' >>>> >>>> Does anyone know how I can work around this? >>>> Thanks, >>>> Eibhlin >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >> _______________________________________________ >> 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 > _______________________________________________ > 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] Running an mpi program that needs to access /dev/mem
by Lee, Eibhlin 13 Jun '13

13 Jun '13

Gus, I believe your first assumption is correct. Unfortunately it just seemed to hang. I think this might be because each one is being made to have the same rank... It may already be obvious but this is the first time I am using Linux. I had tried sudo $(which mpiexec ....) and sudo $(which mpiexec) ... both without success. Is putting the full path to it similar to/is a symlink? (This still doesn't make main have super user privileges though.) Eibhlin ________________________________________ From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf of Gus Correa [gus(a)ldeo.columbia.edu] Sent: 13 June 2013 15:37 To: Discuss Mpich Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem Hi Lee How about replacing "~/main" in the mpiexec command line by one-liner script? Say, "sudo_main.sh", something like this: #! /bin/bash sudo ~/main After all, it is "main" that accesses /dev/mem, and needs "sudo" permissions, not mpiexec, right? [Or do the mpiexec-launched processes inherit the "sudo" stuff from mpiexec?] Not related, but, instead of putting mpiexec in /usr/bin, can't you just use the full path to it? I hope this helps, Gus Correa On 06/13/2013 10:09 AM, Lee, Eibhlin wrote: > Pavan, > I had a lot of trouble getting hydra to work without having to enter a password/passphrase. I saw the option to pass a phrase in the mpich installers guide. I eventually found that for that command you needed to use the smpd process manager. That's the only reason I chose smpd over hydra. > As to your other suggestion. I ran ./main and the same error (Can't open /dev/mem...) appeared. sudo ./main works but of course without multiple processes. > Eibhlin > ________________________________________ > From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf of Pavan Balaji [balaji(a)mcs.anl.gov] > Sent: 13 June 2013 14:34 > To: discuss(a)mpich.org > Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem > > I just saw your older email. Why are you using smpd instead of the > default process manager (hydra)? > > -- Pavan > > On 06/13/2013 08:05 AM, Pavan Balaji wrote: >> >> What's "-phrase"? That's not a recognized option. I'm not sure where >> the /dev/mem check is coming from. Try running ~/main without mpiexec >> first. >> >> -- Pavan >> >> On 06/13/2013 06:56 AM, Lee, Eibhlin wrote: >>> Hello all, >>> >>> I am trying to use two raspberry-pi to sample and then process some >>> data. The first process samples while the second processes and vice >>> versa. To do this I use gpio and also mpich-3.0.4 with the process >>> manager smpd. I have successfully run cpi on both machines (from the >>> master machine). I have also managed to run a similar program but >>> without the MPI, this involved compiling with gcc and when running >>> putting sudo in front of the binary file. >>> >>> When I combine these two processes I get various error messages. >>> For input: >>> mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>> the error is: >>> Can't open /dev/mem >>> Did you forget to use 'sudo .. ?' >>> >>> For input: >>> sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>> the error is: >>> sudo: mpiexec: Command not found >>> >>> I therefore put mpiexec into /usr/bin >>> >>> now for input: >>> sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>> the error is: >>> Can't open /dev/mem >>> Did you forget to use 'sudo .. ?' >>> >>> Does anyone know how I can work around this? >>> Thanks, >>> Eibhlin >>> >>> >>> >>> _______________________________________________ >>> 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 > _______________________________________________ > 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] Running an mpi program that needs to access /dev/mem
by Pavan Balaji 13 Jun '13

13 Jun '13

Try running: % mpiexec [whatever-argument] id This will give you what user id you are running your program as. -- Pavan On 06/13/2013 11:46 AM, Lee, Eibhlin wrote: > It sounds like that won't solve the problem I have. I have run mpiexec as the root user and still get the same problem. > Eibhlin > ________________________________________ > From: Pavan Balaji [balaji(a)mcs.anl.gov] > Sent: 13 June 2013 16:17 > To: Lee, Eibhlin > Cc: discuss(a)mpich.org > Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem > > No. Think of hydra as an ssh program. If you run mpiexec as root, > it'll try to ssh as root. You'll need to make sure ssh as root is > passwordless. > > -- Pavan > > On 06/13/2013 10:08 AM, Lee, Eibhlin wrote: >> My apologies, >> So hydra is in effect a super user? >> Eibhlin >> ________________________________________ >> From: Pavan Balaji [balaji(a)mcs.anl.gov] >> Sent: 13 June 2013 16:02 >> To: Lee, Eibhlin >> Cc: discuss(a)mpich.org >> Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem >> >> Please don't drop the mailing list from the cc. >> >> You can do an strace to see where /dev/mem is being used. >> >> If you are using multiple nodes, hydra only relies on passwordless ssh. >> It doesn't really care what the user id is (root or non-root). >> >> -- Pavan >> >> On 06/13/2013 09:27 AM, Lee, Eibhlin wrote: >>> Unfortunately I didn't come across this mailing list until recently. Sods law. >>> ./main does not work but sudo ./main does work. >>> Could hydra compile and run a program where this is the case? >>> I ask because the only way I'll be able to get around using sudo is to change ownership of /dev/mem. It goes without saying that that's dangerous! >>> Eibhlin >>> ________________________________________ >>> From: Pavan Balaji [balaji(a)mcs.anl.gov] >>> Sent: 13 June 2013 15:21 >>> To: discuss(a)mpich.org >>> Cc: Lee, Eibhlin >>> Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem >>> >>> smpd was mainly meant for windows support. It is now deprecated, so we >>> don't officially support that. Someone on the mailing list might help, >>> but no promises. >>> >>> With respect to hydra, problems with that is what you should have >>> reported on this mailing list and we would have tried to help. :-) >>> >>> If ./main itself is not working, there's no hope of getting it to work >>> with mpiexec. You'll need to debug that first. >>> >>> -- Pavan >>> >>> On 06/13/2013 09:09 AM, Lee, Eibhlin wrote: >>>> Pavan, >>>> I had a lot of trouble getting hydra to work without having to enter a password/passphrase. I saw the option to pass a phrase in the mpich installers guide. I eventually found that for that command you needed to use the smpd process manager. That's the only reason I chose smpd over hydra. >>>> As to your other suggestion. I ran ./main and the same error (Can't open /dev/mem...) appeared. sudo ./main works but of course without multiple processes. >>>> Eibhlin >>>> ________________________________________ >>>> From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf of Pavan Balaji [balaji(a)mcs.anl.gov] >>>> Sent: 13 June 2013 14:34 >>>> To: discuss(a)mpich.org >>>> Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem >>>> >>>> I just saw your older email. Why are you using smpd instead of the >>>> default process manager (hydra)? >>>> >>>> -- Pavan >>>> >>>> On 06/13/2013 08:05 AM, Pavan Balaji wrote: >>>>> >>>>> What's "-phrase"? That's not a recognized option. I'm not sure where >>>>> the /dev/mem check is coming from. Try running ~/main without mpiexec >>>>> first. >>>>> >>>>> -- Pavan >>>>> >>>>> On 06/13/2013 06:56 AM, Lee, Eibhlin wrote: >>>>>> Hello all, >>>>>> >>>>>> I am trying to use two raspberry-pi to sample and then process some >>>>>> data. The first process samples while the second processes and vice >>>>>> versa. To do this I use gpio and also mpich-3.0.4 with the process >>>>>> manager smpd. I have successfully run cpi on both machines (from the >>>>>> master machine). I have also managed to run a similar program but >>>>>> without the MPI, this involved compiling with gcc and when running >>>>>> putting sudo in front of the binary file. >>>>>> >>>>>> When I combine these two processes I get various error messages. >>>>>> For input: >>>>>> mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>>>>> the error is: >>>>>> Can't open /dev/mem >>>>>> Did you forget to use 'sudo .. ?' >>>>>> >>>>>> For input: >>>>>> sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>>>>> the error is: >>>>>> sudo: mpiexec: Command not found >>>>>> >>>>>> I therefore put mpiexec into /usr/bin >>>>>> >>>>>> now for input: >>>>>> sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>>>>> the error is: >>>>>> Can't open /dev/mem >>>>>> Did you forget to use 'sudo .. ?' >>>>>> >>>>>> Does anyone know how I can work around this? >>>>>> Thanks, >>>>>> Eibhlin >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>> _______________________________________________ >>>> 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 >>>> >>> >>> -- >>> Pavan Balaji >>> http://www.mcs.anl.gov/~balaji >>> >> >> -- >> Pavan Balaji >> http://www.mcs.anl.gov/~balaji >> > > -- > Pavan Balaji > http://www.mcs.anl.gov/~balaji > -- Pavan Balaji http://www.mcs.anl.gov/~balaji

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Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem
by Lee, Eibhlin 13 Jun '13

13 Jun '13

It sounds like that won't solve the problem I have. I have run mpiexec as the root user and still get the same problem. Eibhlin ________________________________________ From: Pavan Balaji [balaji(a)mcs.anl.gov] Sent: 13 June 2013 16:17 To: Lee, Eibhlin Cc: discuss(a)mpich.org Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem No. Think of hydra as an ssh program. If you run mpiexec as root, it'll try to ssh as root. You'll need to make sure ssh as root is passwordless. -- Pavan On 06/13/2013 10:08 AM, Lee, Eibhlin wrote: > My apologies, > So hydra is in effect a super user? > Eibhlin > ________________________________________ > From: Pavan Balaji [balaji(a)mcs.anl.gov] > Sent: 13 June 2013 16:02 > To: Lee, Eibhlin > Cc: discuss(a)mpich.org > Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem > > Please don't drop the mailing list from the cc. > > You can do an strace to see where /dev/mem is being used. > > If you are using multiple nodes, hydra only relies on passwordless ssh. > It doesn't really care what the user id is (root or non-root). > > -- Pavan > > On 06/13/2013 09:27 AM, Lee, Eibhlin wrote: >> Unfortunately I didn't come across this mailing list until recently. Sods law. >> ./main does not work but sudo ./main does work. >> Could hydra compile and run a program where this is the case? >> I ask because the only way I'll be able to get around using sudo is to change ownership of /dev/mem. It goes without saying that that's dangerous! >> Eibhlin >> ________________________________________ >> From: Pavan Balaji [balaji(a)mcs.anl.gov] >> Sent: 13 June 2013 15:21 >> To: discuss(a)mpich.org >> Cc: Lee, Eibhlin >> Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem >> >> smpd was mainly meant for windows support. It is now deprecated, so we >> don't officially support that. Someone on the mailing list might help, >> but no promises. >> >> With respect to hydra, problems with that is what you should have >> reported on this mailing list and we would have tried to help. :-) >> >> If ./main itself is not working, there's no hope of getting it to work >> with mpiexec. You'll need to debug that first. >> >> -- Pavan >> >> On 06/13/2013 09:09 AM, Lee, Eibhlin wrote: >>> Pavan, >>> I had a lot of trouble getting hydra to work without having to enter a password/passphrase. I saw the option to pass a phrase in the mpich installers guide. I eventually found that for that command you needed to use the smpd process manager. That's the only reason I chose smpd over hydra. >>> As to your other suggestion. I ran ./main and the same error (Can't open /dev/mem...) appeared. sudo ./main works but of course without multiple processes. >>> Eibhlin >>> ________________________________________ >>> From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf of Pavan Balaji [balaji(a)mcs.anl.gov] >>> Sent: 13 June 2013 14:34 >>> To: discuss(a)mpich.org >>> Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem >>> >>> I just saw your older email. Why are you using smpd instead of the >>> default process manager (hydra)? >>> >>> -- Pavan >>> >>> On 06/13/2013 08:05 AM, Pavan Balaji wrote: >>>> >>>> What's "-phrase"? That's not a recognized option. I'm not sure where >>>> the /dev/mem check is coming from. Try running ~/main without mpiexec >>>> first. >>>> >>>> -- Pavan >>>> >>>> On 06/13/2013 06:56 AM, Lee, Eibhlin wrote: >>>>> Hello all, >>>>> >>>>> I am trying to use two raspberry-pi to sample and then process some >>>>> data. The first process samples while the second processes and vice >>>>> versa. To do this I use gpio and also mpich-3.0.4 with the process >>>>> manager smpd. I have successfully run cpi on both machines (from the >>>>> master machine). I have also managed to run a similar program but >>>>> without the MPI, this involved compiling with gcc and when running >>>>> putting sudo in front of the binary file. >>>>> >>>>> When I combine these two processes I get various error messages. >>>>> For input: >>>>> mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>>>> the error is: >>>>> Can't open /dev/mem >>>>> Did you forget to use 'sudo .. ?' >>>>> >>>>> For input: >>>>> sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>>>> the error is: >>>>> sudo: mpiexec: Command not found >>>>> >>>>> I therefore put mpiexec into /usr/bin >>>>> >>>>> now for input: >>>>> sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>>>> the error is: >>>>> Can't open /dev/mem >>>>> Did you forget to use 'sudo .. ?' >>>>> >>>>> Does anyone know how I can work around this? >>>>> Thanks, >>>>> Eibhlin >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>> _______________________________________________ >>> 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 >>> >> >> -- >> Pavan Balaji >> http://www.mcs.anl.gov/~balaji >> > > -- > Pavan Balaji > http://www.mcs.anl.gov/~balaji > -- Pavan Balaji http://www.mcs.anl.gov/~balaji

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Re: [mpich-discuss] install + config on windows
by Jayesh Krishna 13 Jun '13

13 Jun '13

Hi, >> ...actually, it seems that Mpich must be compiled to work... You shouldn't have to build MPICH2 on Windows to run your MPI programs. You should be able to install MPICH2 on your system using the msi files provided in the MPICH website (However, if you are using a 3rd party software compiled using MPICH2 you need to install the same version of MPICH on your system - ask the developers of the software for the version of MPICH). Since you are using Windows 7, you need to make sure that you install MPICH2 from an administrator command prompt (Uninstall any versions of MPICH2 installed in your system and follow guidelines in the installer's guide to install MPICH2). As Antonio mentioned we just don't have the developer bandwidth to keep the Windows part of code in MPICH up to date. So if you need to use MPICH2 on Windows please use the older versions of MPICH2 available on the MPICH website. Regards, Jayesh ----- Original Message ----- From: "Antonio J. Peña" <apenya(a)mcs.anl.gov> To: geo(a)spatiogis.fr, discuss(a)mpich.org Sent: Tuesday, June 11, 2013 5:17:20 PM Subject: Re: [mpich-discuss] install + config on windows Hi Benoit, As our support for Windows platforms has been discontinued, we cannot guarantee MPICH is going to be able to be compiled in newer versions of the Windows compilers and/or the operating system itself. Unless Jayesh has any comments on this regard, I'm not aware of any experience of MPICH + Windows 7. I apologize for the inconvenience. Thanks, Antonio On Monday, June 10, 2013 08:04:03 AM spatiogis wrote: > Hello, > > actually, it seems that Mpich must be compiled to work. The point is that > the "Readme" file gives an explanation to compile the programs with Visual > studio 2003. Anyway this last software is very difficult to make work on > windows 7. > > Is there finally a way to compile Mpich on windows 7 with Visual Studio ? > > best regards, > > Benoit Véler > > > Hi, > > > > From the log output it looks like credentials (password) for > > > > Utilisateur was not correct. > > > > Is Utilisateur a valid Windows user on your machine? Have you > > > > registered the username/password correctly (Try re-registering the > > username+password by typing "mpiexec -register" at the command prompt)? > > > > Regards, > > Jayesh > > > > ----- Original Message ----- > > From: "spatiogis" <geo(a)spatiogis.fr> > > To: discuss(a)mpich.org > > Sent: Friday, May 3, 2013 11:58:00 AM > > Subject: Re: [mpich-discuss] install + config on windows > > > > Hello, > > > > for this command : > > > > # C:\Progra~1\MPICH2\bin\mpiexec -verbose -n 2 > > > > C:\Progra~1\MPICH2\examples\cpi.exe > > > > result : > > > > ....../SMPDU_Sock_post_readv > > > > ...../SMPDU_Sock_post_read > > ..../smpd_handle_op_connect > > ....sock_waiting for the next event. > > ....\SMPDU_Sock_wait > > ..../SMPDU_Sock_wait > > ....SOCK_OP_READ event.error = 0, result = 0, context=left > > ....\smpd_handle_op_read > > .....\smpd_state_reading_challenge_string > > ......read challenge string: '1.4.1p1 18467' > > ......\smpd_verify_version > > ....../smpd_verify_version > > ......Verification of smpd version succeeded > > ......\smpd_hash > > ....../smpd_hash > > ......\SMPDU_Sock_post_write > > .......\SMPDU_Sock_post_writev > > ......./SMPDU_Sock_post_writev > > ....../SMPDU_Sock_post_write > > ...../smpd_state_reading_challenge_string > > ..../smpd_handle_op_read > > ....sock_waiting for the next event. > > ....\SMPDU_Sock_wait > > ..../SMPDU_Sock_wait > > ....SOCK_OP_WRITE event.error = 0, result = 0, context=left > > ....\smpd_handle_op_write > > .....\smpd_state_writing_challenge_response > > ......wrote challenge response: 'dafd1d07c1e6e9cb5fae968403d0d933' > > ......\SMPDU_Sock_post_read > > .......\SMPDU_Sock_post_readv > > ......./SMPDU_Sock_post_readv > > ....../SMPDU_Sock_post_read > > ...../smpd_state_writing_challenge_response > > ..../smpd_handle_op_write > > ....sock_waiting for the next event. > > ....\SMPDU_Sock_wait > > ..../SMPDU_Sock_wait > > ....SOCK_OP_READ event.error = 0, result = 0, context=left > > ....\smpd_handle_op_read > > .....\smpd_state_reading_connect_result > > ......read connect result: 'SUCCESS' > > ......\SMPDU_Sock_post_write > > .......\SMPDU_Sock_post_writev > > ......./SMPDU_Sock_post_writev > > ....../SMPDU_Sock_post_write > > ...../smpd_state_reading_connect_result > > ..../smpd_handle_op_read > > ....sock_waiting for the next event. > > ....\SMPDU_Sock_wait > > ..../SMPDU_Sock_wait > > ....SOCK_OP_WRITE event.error = 0, result = 0, context=left > > ....\smpd_handle_op_write > > .....\smpd_state_writing_process_session_request > > ......wrote process session request: 'process' > > ......\SMPDU_Sock_post_read > > .......\SMPDU_Sock_post_readv > > ......./SMPDU_Sock_post_readv > > ....../SMPDU_Sock_post_read > > ...../smpd_state_writing_process_session_request > > ..../smpd_handle_op_write > > ....sock_waiting for the next event. > > ....\SMPDU_Sock_wait > > ..../SMPDU_Sock_wait > > ....SOCK_OP_READ event.error = 0, result = 0, context=left > > ....\smpd_handle_op_read > > .....\smpd_state_reading_cred_request > > ......read cred request: 'credentials' > > ......\smpd_hide_string_arg > > .......\first_token > > ......./first_token > > .......\compare_token > > ......./compare_token > > .......\next_token > > ........\first_token > > ......../first_token > > ........\first_token > > ......../first_token > > ......./next_token > > ....../smpd_hide_string_arg > > ....../smpd_hide_string_arg > > ......\smpd_hide_string_arg > > .......\first_token > > ......./first_token > > .......\compare_token > > ......./compare_token > > .......\next_token > > ........\first_token > > ......../first_token > > ........\first_token > > ......../first_token > > ......./next_token > > ....../smpd_hide_string_arg > > ....../smpd_hide_string_arg > > ......\smpd_hide_string_arg > > .......\first_token > > ......./first_token > > .......\compare_token > > ......./compare_token > > .......\next_token > > ........\first_token > > ......../first_token > > ........\first_token > > ......../first_token > > ......./next_token > > ....../smpd_hide_string_arg > > ....../smpd_hide_string_arg > > ......\smpd_hide_string_arg > > .......\first_token > > ......./first_token > > .......\compare_token > > ......./compare_token > > .......\next_token > > ........\first_token > > ......../first_token > > ........\first_token > > ......../first_token > > ......./next_token > > ....../smpd_hide_string_arg > > ....../smpd_hide_string_arg > > ......\smpd_hide_string_arg > > .......\first_token > > ......./first_token > > .......\compare_token > > ......./compare_token > > .......\next_token > > ........\first_token > > ......../first_token > > ........\first_token > > ......../first_token > > ......./next_token > > ....../smpd_hide_string_arg > > ....../smpd_hide_string_arg > > .......\smpd_option_on > > ........\smpd_get_smpd_data > > .........\smpd_get_smpd_data_from_environment > > ........./smpd_get_smpd_data_from_environment > > .........\smpd_get_smpd_data_default > > ........./smpd_get_smpd_data_default > > .........Unable to get the data for the key 'nocache' > > ......../smpd_get_smpd_data > > ......./smpd_option_on > > ......\smpd_hide_string_arg > > .......\first_token > > ......./first_token > > .......\compare_token > > ......./compare_token > > .......\next_token > > ........\first_token > > ......../first_token > > ........\first_token > > ......../first_token > > ......./next_token > > ....../smpd_hide_string_arg > > ....../smpd_hide_string_arg > > ......\SMPDU_Sock_post_write > > .......\SMPDU_Sock_post_writev > > ......./SMPDU_Sock_post_writev > > ....../SMPDU_Sock_post_write > > ...../smpd_handle_op_read > > .....sock_waiting for the next event. > > .....\SMPDU_Sock_wait > > ...../SMPDU_Sock_wait > > .....SOCK_OP_WRITE event.error = 0, result = 0, context=left > > .....\smpd_handle_op_write > > ......\smpd_state_writing_cred_ack_yes > > .......wrote cred request yes ack. > > .......\SMPDU_Sock_post_write > > ........\SMPDU_Sock_post_writev > > ......../SMPDU_Sock_post_writev > > ......./SMPDU_Sock_post_write > > ....../smpd_state_writing_cred_ack_yes > > ...../smpd_handle_op_write > > .....sock_waiting for the next event. > > .....\SMPDU_Sock_wait > > ...../SMPDU_Sock_wait > > .....SOCK_OP_WRITE event.error = 0, result = 0, context=left > > .....\smpd_handle_op_write > > ......\smpd_state_writing_account > > .......wrote account: 'Utilisateur' > > .......\smpd_encrypt_data > > ......./smpd_encrypt_data > > .......\SMPDU_Sock_post_write > > ........\SMPDU_Sock_post_writev > > ......../SMPDU_Sock_post_writev > > ......./SMPDU_Sock_post_write > > ....../smpd_state_writing_account > > ...../smpd_handle_op_write > > .....sock_waiting for the next event. > > .....\SMPDU_Sock_wait > > ...../SMPDU_Sock_wait > > .....SOCK_OP_WRITE event.error = 0, result = 0, context=left > > .....\smpd_handle_op_write > > ......\smpd_hide_string_arg > > .......\first_token > > ......./first_token > > .......\compare_token > > ......./compare_token > > .......\next_token > > ........\first_token > > ......../first_token > > ........\first_token > > ......../first_token > > ......./next_token > > ....../smpd_hide_string_arg > > ....../smpd_hide_string_arg > > .......\smpd_hide_string_arg > > ........\first_token > > ......../first_token > > ........\compare_token > > ......../compare_token > > ........\next_token > > .........\first_token > > ........./first_token > > .........\first_token > > ........./first_token > > ......../next_token > > ......./smpd_hide_string_arg > > ......./smpd_hide_string_arg > > .......\SMPDU_Sock_post_read > > ........\SMPDU_Sock_post_readv > > ......../SMPDU_Sock_post_readv > > ......./SMPDU_Sock_post_read > > ......\smpd_hide_string_arg > > .......\first_token > > ......./first_token > > .......\compare_token > > ......./compare_token > > .......\next_token > > ........\first_token > > ......../first_token > > ........\first_token > > ......../first_token > > ......./next_token > > ....../smpd_hide_string_arg > > ....../smpd_hide_string_arg > > ...../smpd_handle_op_write > > .....sock_waiting for the next event. > > .....\SMPDU_Sock_wait > > ...../SMPDU_Sock_wait > > .....SOCK_OP_READ event.error = 0, result = 0, context=left > > .....\smpd_handle_op_read > > ......\smpd_state_reading_process_result > > .......read process session result: 'FAIL' > > .......\smpd_hide_string_arg > > ........\first_token > > ......../first_token > > ........\compare_token > > ......../compare_token > > ........\next_token > > .........\first_token > > ........./first_token > > .........\first_token > > ........./first_token > > ......../next_token > > ......./smpd_hide_string_arg > > ......./smpd_hide_string_arg > > .......\smpd_hide_string_arg > > ........\first_token > > ......../first_token > > ........\compare_token > > ......../compare_token > > ........\next_token > > .........\first_token > > ........./first_token > > .........\first_token > > ........./first_token > > ......../next_token > > ......./smpd_hide_string_arg > > ......./smpd_hide_string_arg > > Credentials for Utilisateur rejected connecting to Benoit > > .......process session rejected > > .......\SMPDU_Sock_post_close > > ........\SMPDU_Sock_post_read > > .........\SMPDU_Sock_post_readv > > ........./SMPDU_Sock_post_readv > > ......../SMPDU_Sock_post_read > > ......./SMPDU_Sock_post_close > > .......\smpd_post_abort_command > > ........\smpd_create_command > > .........\smpd_init_command > > ........./smpd_init_command > > ......../smpd_create_command > > ........\smpd_add_command_arg > > ......../smpd_add_command_arg > > ........\smpd_command_destination > > .........0 -> 0 : returning NULL context > > ......../smpd_command_destination > > Aborting: Unable to connect to Benoit > > ......./smpd_post_abort_command > > .......\smpd_exit > > ........\smpd_kill_all_processes > > ......../smpd_kill_all_processes > > ........\smpd_finalize_drive_maps > > ......../smpd_finalize_drive_maps > > ........\smpd_dbs_finalize > > ......../smpd_dbs_finalize > > ........\SMPDU_Sock_finalize > > ......../SMPDU_Sock_finalize > > > > C:\Users\Utilisateur> > > > >> Hi, > >> > >> Looks like you missed the "-" before the status ("smpd -status" not > >> > >> "smpd status") argument. > >> > >> It also looks like you have multiple MPI libraries installed in your > >> > >> system. Try running this command (full path to mpiexec and smpd), > >> > >> # C:\Progra~1\MPICH2\bin\smpd -status > >> > >> # C:\Progra~1\MPICH2\bin\mpiexec -verbose -n 2 > >> C:\Progra~1\MPICH2\examples\cpi.exe > >> > >> > >> Regards, > >> Jayesh > >> > >> ----- Original Message ----- > >> From: "spatiogis" <geo(a)spatiogis.fr> > >> To: "Jayesh Krishna" <jayesh(a)mcs.anl.gov> > >> Sent: Friday, May 3, 2013 11:05:34 AM > >> Subject: Re: [mpich-discuss] install + config on windows > >> > >> Hello, > >> > >> C:\Users\Utilisateur>smpd status > >> Unexpected parameters: status > >> > >> C:\Users\Utilisateur>mpiexec -verbose -n 2 > >> C:\Progra~1\MPICH2\examples\cpi.exe > >> Unknown option: -verbose > >> > >> ------------------------------------------------------------------------- > >> ---- C:\Program Files\MPICH2\examples>mpiexec -verbose -n 2 cpi.exe > >> Unknown option: -verbose > >> > >> C:\Program Files\MPICH2\examples>smpd status > >> Unexpected parameters: status > >> ------------------------------------------------------------------------- > >> ---- > >> > >> regards, Ben > >> > >>> Hi, > >>> > >>> Ok. Please send us the output of the following commands, > >>> > >>> # smpd -status > >>> # mpiexec -verbose -n 2 C:\Progra~1\MPICH2\examples\cpi.exe > >>> > >>> Please copy-paste the command and the complete output in your email. > >>> > >>> Regards, > >>> Jayesh > >>> > >>> > >>> ----- Original Message ----- > >>> From: "spatiogis" <geo(a)spatiogis.fr> > >>> To: discuss(a)mpich.org > >>> Sent: Friday, May 3, 2013 1:46:53 AM > >>> Subject: Re: [mpich-discuss] install + config on windows > >>> > >>> Hello > >>> > >>>> (PS: I am assuming from your reply in the previous email that you can > >>>> run a command like "mpiexec -n 2 C:\Progra~1\MPICH2\examples\cpi.exe" > >>>> correctly) > >>>> > >>> In fact this command doesn't run. > >>> > >>> The message is this one > >>> > >>> [01:11728]....ERROR:unable to read the cmd header on the pmi context, > >>> > >>> Error = -1 > >>> > >>> Ben > >>> > >>>> ----- Original Message ----- > >>>> From: "spatiogis" <geo(a)spatiogis.fr> > >>>> To: "Jayesh Krishna" <jayesh(a)mcs.anl.gov> > >>>> Sent: Thursday, May 2, 2013 10:48:56 AM > >>>> Subject: Re: [mpich-discuss] install + config on windows > >>>> > >>>> Hello, > >>>> > >>>>> Hi, > >>>>> > >>>>> Are you able to run any other MPI programs? Try running the example > >>>>> > >>>>> program, cpi.exe (C:\Program Files\MPICH2\examples\cpi.exe), to make > >>>>> sure that your MPICH2 installation works. > >>>>> > >>>> yes it does work > >>>> > >>>>> Installing MPICH2 on Windows 7 typically requires you to uninstall > >>>>> > >>>>> any > >>>>> previous versions of MPICH2, launch an administrative command promt > >>>>> and > >>>>> run "msiexec /i mpich2-installer.msi" to install MPICH2. > >>>>> > >>>> yes it 's been installed like this... > >>>> > >>>> In wmpiconfig, the message is the following in the 'Get settings' > >>>> > >>>> line. > >>>> > >>>> Credentials for Utilisateur rejected connecting to host > >>>> Aborting: Unable to connect to host > >>>> > >>>> The software I try to use is Taudem, which is intergrated inside > >>>> > >>>> Qgis. > >>>> Launching a taudem process inside Qgis gives the same message. > >>>> > >>>>> Regards, > >>>>> Jayesh > >>>>> > >>>> Sincerely, Ben > >>>> > >>>>> ----- Original Message ----- > >>>>> From: "spatiogis" <geo(a)spatiogis.fr> > >>>>> To: discuss(a)mpich.org > >>>>> Sent: Thursday, May 2, 2013 10:08:23 AM > >>>>> Subject: Re: [mpich-discuss] install + config on windows > >>>>> > >>>>> Hello, > >>>>> > >>>>> in my case Mpich is normally used to run .exe programs. I guess that > >>>>> > >>>>> they > >>>>> are already compiled... > >>>>> > >>>>> The .exe files are integrated into a software, and accessed from > >>>>> > >>>>> menus > >>>>> inside it. When I run one of the programs, the answer is actually > >>>>> "unable > >>>>> to query host". > >>>>> > >>>>> At the end, the process is not realised. It seems that this 'host' > >>>>> > >>>>> question is a problem to the software... > >>>>> > >>>>> Sincerely, > >>>>> > >>>>> Ben. > >>>>> > >>>>>> Hi, > >>>>>> > >>>>>> You can download MPICH2 binaries for Windows at > >>>>>> > >>>>>> http://www.mpich.org/downloads/ . > >>>>>> > >>>>>> You need to compile your MPI programs with MPICH2 to make it work. > >>>>>> > >>>>>> I > >>>>>> would recommend recompiling your code after you install MPICH2 (If > >>>>>> you > >>>>>> have MPI program binaries pre-built with MPICH2 - instead of > >>>>>> compiling > >>>>>> them on your own - make sure that you install the same version of > >>>>>> MPICH2 > >>>>>> that was used to build the binaries). > >>>>>> > >>>>>> The wmpiregister program has a bug and you can ignore this error > >>>>>> > >>>>>> message ("...unable to query host"). Can you run your MPI program > >>>>>> using > >>>>>> mpiexec from a command prompt? > >>>>>> > >>>>>> Regards, > >>>>>> Jayesh > >>>>>> > >>>>>> ----- Original Message ----- > >>>>>> From: "spatiogis" <geo(a)spatiogis.fr> > >>>>>> To: discuss(a)mpich.org > >>>>>> Sent: Tuesday, April 30, 2013 9:26:35 AM > >>>>>> Subject: [mpich-discuss] install + config on windows > >>>>>> > >>>>>> Hello, > >>>>>> > >>>>>> I'm not very good at computing, but I would like to install Mpich2 > >>>>>> > >>>>>> on > >>>>>> windows 7 - 64 bits. There is only one pc, with one user plus the > >>>>>> admin, > >>>>>> and a simple core processor. > >>>>>> > >>>>>> I would like to know if it's mandatory to have compiling softwares > >>>>>> > >>>>>> with > >>>>>> it to make it work, whereas it is asked in this case only to make > >>>>>> run > >>>>>> another software, and not for compiling (that would maybe save some > >>>>>> disk > >>>>>> space and simplify the installation) ? > >>>>>> > >>>>>> My second issue is that I must be missing something about the > >>>>>> > >>>>>> server > >>>>>> configuration. I have installed Mpich from the .msi file, then > >>>>>> configured > >>>>>> the wmpiregister program with the Domain/user informations. > >>>>>> > >>>>>> There is this message displayed when trying to connect in the > >>>>>> > >>>>>> 'configurable settings' window : 'MPICH2 not installed or unable to > >>>>>> query > >>>>>> the host'. > >>>>>> > >>>>>> What is the host actually ? > >>>>>> > >>>>>> I know I am starting from very far, I am sorry for these very > >>>>>> > >>>>>> simple > >>>>>> questions. Thanks if you can reply me, that would certainly save me > >>>>>> some > >>>>>> long hours of reading and testing ;) > >>>>>> > >>>>>> sincerely, > >>>>>> > >>>>>> Ben > >>>>>> > >>>>>> _______________________________________________ > >>>>>> 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] How to keep the VS console window open on exceptions during debug of a parallel code
by Antonio J. Peña 13 Jun '13

13 Jun '13

Dear Feng Xiao, Unfortunately we discontinued support for Windows some time ago. In addition, our Windows expert is no longer working in our team. If you need support on Windows, I'd suggest considering using some other implementation. I hope some other user subscribed to this list can help you. Best, Antonio On Thursday, June 13, 2013 07:31:09 AM Feng Xiao wrote: Hello, I am writing about how to keep the console window open on exceptions during debug of a parallel code (either F5 or Ctrl+F5). I am running MPICH2 FORTRAN program in Visual Studio 2010, everything works fine, expect that I could not see the exception/error messages on the console window, it closes right after the program exits on exceptions. I do know how to keep the console window open when program meets the end, or put a read statement to pause the program during the execution. I did some google search, the only relevant solution I could find is http://www.boost.org/doc/libs/1_36_0/libs/test/doc/html/utf/usage-recommend…, which is about making debugger break at the point the failure by adding extra command line argument and seeing the runtime error in the output window. However, it looks like something for a serial code without mpiexec.exe in the command line, and I am not a advanced VS user, so I don't know how to do it for a parallel code, or if there is any other way out. Thanks in advance! -- Feng Xiao Doctoral Student Petroleum Engineering Colorado School of Mines Cell 918-814-2644 -------- [1] http://www.boost.org/doc/libs/1_36_0/libs/test/doc/html/utf/usage-recommend…

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Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem
by Pavan Balaji 13 Jun '13

13 Jun '13

No. Think of hydra as an ssh program. If you run mpiexec as root, it'll try to ssh as root. You'll need to make sure ssh as root is passwordless. -- Pavan On 06/13/2013 10:08 AM, Lee, Eibhlin wrote: > My apologies, > So hydra is in effect a super user? > Eibhlin > ________________________________________ > From: Pavan Balaji [balaji(a)mcs.anl.gov] > Sent: 13 June 2013 16:02 > To: Lee, Eibhlin > Cc: discuss(a)mpich.org > Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem > > Please don't drop the mailing list from the cc. > > You can do an strace to see where /dev/mem is being used. > > If you are using multiple nodes, hydra only relies on passwordless ssh. > It doesn't really care what the user id is (root or non-root). > > -- Pavan > > On 06/13/2013 09:27 AM, Lee, Eibhlin wrote: >> Unfortunately I didn't come across this mailing list until recently. Sods law. >> ./main does not work but sudo ./main does work. >> Could hydra compile and run a program where this is the case? >> I ask because the only way I'll be able to get around using sudo is to change ownership of /dev/mem. It goes without saying that that's dangerous! >> Eibhlin >> ________________________________________ >> From: Pavan Balaji [balaji(a)mcs.anl.gov] >> Sent: 13 June 2013 15:21 >> To: discuss(a)mpich.org >> Cc: Lee, Eibhlin >> Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem >> >> smpd was mainly meant for windows support. It is now deprecated, so we >> don't officially support that. Someone on the mailing list might help, >> but no promises. >> >> With respect to hydra, problems with that is what you should have >> reported on this mailing list and we would have tried to help. :-) >> >> If ./main itself is not working, there's no hope of getting it to work >> with mpiexec. You'll need to debug that first. >> >> -- Pavan >> >> On 06/13/2013 09:09 AM, Lee, Eibhlin wrote: >>> Pavan, >>> I had a lot of trouble getting hydra to work without having to enter a password/passphrase. I saw the option to pass a phrase in the mpich installers guide. I eventually found that for that command you needed to use the smpd process manager. That's the only reason I chose smpd over hydra. >>> As to your other suggestion. I ran ./main and the same error (Can't open /dev/mem...) appeared. sudo ./main works but of course without multiple processes. >>> Eibhlin >>> ________________________________________ >>> From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf of Pavan Balaji [balaji(a)mcs.anl.gov] >>> Sent: 13 June 2013 14:34 >>> To: discuss(a)mpich.org >>> Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem >>> >>> I just saw your older email. Why are you using smpd instead of the >>> default process manager (hydra)? >>> >>> -- Pavan >>> >>> On 06/13/2013 08:05 AM, Pavan Balaji wrote: >>>> >>>> What's "-phrase"? That's not a recognized option. I'm not sure where >>>> the /dev/mem check is coming from. Try running ~/main without mpiexec >>>> first. >>>> >>>> -- Pavan >>>> >>>> On 06/13/2013 06:56 AM, Lee, Eibhlin wrote: >>>>> Hello all, >>>>> >>>>> I am trying to use two raspberry-pi to sample and then process some >>>>> data. The first process samples while the second processes and vice >>>>> versa. To do this I use gpio and also mpich-3.0.4 with the process >>>>> manager smpd. I have successfully run cpi on both machines (from the >>>>> master machine). I have also managed to run a similar program but >>>>> without the MPI, this involved compiling with gcc and when running >>>>> putting sudo in front of the binary file. >>>>> >>>>> When I combine these two processes I get various error messages. >>>>> For input: >>>>> mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>>>> the error is: >>>>> Can't open /dev/mem >>>>> Did you forget to use 'sudo .. ?' >>>>> >>>>> For input: >>>>> sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>>>> the error is: >>>>> sudo: mpiexec: Command not found >>>>> >>>>> I therefore put mpiexec into /usr/bin >>>>> >>>>> now for input: >>>>> sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>>>> the error is: >>>>> Can't open /dev/mem >>>>> Did you forget to use 'sudo .. ?' >>>>> >>>>> Does anyone know how I can work around this? >>>>> Thanks, >>>>> Eibhlin >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>> _______________________________________________ >>> 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 >>> >> >> -- >> Pavan Balaji >> http://www.mcs.anl.gov/~balaji >> > > -- > Pavan Balaji > http://www.mcs.anl.gov/~balaji > -- Pavan Balaji http://www.mcs.anl.gov/~balaji

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Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem
by Lee, Eibhlin 13 Jun '13

13 Jun '13

My apologies, So hydra is in effect a super user? Eibhlin ________________________________________ From: Pavan Balaji [balaji(a)mcs.anl.gov] Sent: 13 June 2013 16:02 To: Lee, Eibhlin Cc: discuss(a)mpich.org Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem Please don't drop the mailing list from the cc. You can do an strace to see where /dev/mem is being used. If you are using multiple nodes, hydra only relies on passwordless ssh. It doesn't really care what the user id is (root or non-root). -- Pavan On 06/13/2013 09:27 AM, Lee, Eibhlin wrote: > Unfortunately I didn't come across this mailing list until recently. Sods law. > ./main does not work but sudo ./main does work. > Could hydra compile and run a program where this is the case? > I ask because the only way I'll be able to get around using sudo is to change ownership of /dev/mem. It goes without saying that that's dangerous! > Eibhlin > ________________________________________ > From: Pavan Balaji [balaji(a)mcs.anl.gov] > Sent: 13 June 2013 15:21 > To: discuss(a)mpich.org > Cc: Lee, Eibhlin > Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem > > smpd was mainly meant for windows support. It is now deprecated, so we > don't officially support that. Someone on the mailing list might help, > but no promises. > > With respect to hydra, problems with that is what you should have > reported on this mailing list and we would have tried to help. :-) > > If ./main itself is not working, there's no hope of getting it to work > with mpiexec. You'll need to debug that first. > > -- Pavan > > On 06/13/2013 09:09 AM, Lee, Eibhlin wrote: >> Pavan, >> I had a lot of trouble getting hydra to work without having to enter a password/passphrase. I saw the option to pass a phrase in the mpich installers guide. I eventually found that for that command you needed to use the smpd process manager. That's the only reason I chose smpd over hydra. >> As to your other suggestion. I ran ./main and the same error (Can't open /dev/mem...) appeared. sudo ./main works but of course without multiple processes. >> Eibhlin >> ________________________________________ >> From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf of Pavan Balaji [balaji(a)mcs.anl.gov] >> Sent: 13 June 2013 14:34 >> To: discuss(a)mpich.org >> Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem >> >> I just saw your older email. Why are you using smpd instead of the >> default process manager (hydra)? >> >> -- Pavan >> >> On 06/13/2013 08:05 AM, Pavan Balaji wrote: >>> >>> What's "-phrase"? That's not a recognized option. I'm not sure where >>> the /dev/mem check is coming from. Try running ~/main without mpiexec >>> first. >>> >>> -- Pavan >>> >>> On 06/13/2013 06:56 AM, Lee, Eibhlin wrote: >>>> Hello all, >>>> >>>> I am trying to use two raspberry-pi to sample and then process some >>>> data. The first process samples while the second processes and vice >>>> versa. To do this I use gpio and also mpich-3.0.4 with the process >>>> manager smpd. I have successfully run cpi on both machines (from the >>>> master machine). I have also managed to run a similar program but >>>> without the MPI, this involved compiling with gcc and when running >>>> putting sudo in front of the binary file. >>>> >>>> When I combine these two processes I get various error messages. >>>> For input: >>>> mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>>> the error is: >>>> Can't open /dev/mem >>>> Did you forget to use 'sudo .. ?' >>>> >>>> For input: >>>> sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>>> the error is: >>>> sudo: mpiexec: Command not found >>>> >>>> I therefore put mpiexec into /usr/bin >>>> >>>> now for input: >>>> sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>>> the error is: >>>> Can't open /dev/mem >>>> Did you forget to use 'sudo .. ?' >>>> >>>> Does anyone know how I can work around this? >>>> Thanks, >>>> Eibhlin >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >> _______________________________________________ >> 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 >> > > -- > Pavan Balaji > http://www.mcs.anl.gov/~balaji > -- Pavan Balaji http://www.mcs.anl.gov/~balaji

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Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem
by Pavan Balaji 13 Jun '13

13 Jun '13

Please don't drop the mailing list from the cc. You can do an strace to see where /dev/mem is being used. If you are using multiple nodes, hydra only relies on passwordless ssh. It doesn't really care what the user id is (root or non-root). -- Pavan On 06/13/2013 09:27 AM, Lee, Eibhlin wrote: > Unfortunately I didn't come across this mailing list until recently. Sods law. > ./main does not work but sudo ./main does work. > Could hydra compile and run a program where this is the case? > I ask because the only way I'll be able to get around using sudo is to change ownership of /dev/mem. It goes without saying that that's dangerous! > Eibhlin > ________________________________________ > From: Pavan Balaji [balaji(a)mcs.anl.gov] > Sent: 13 June 2013 15:21 > To: discuss(a)mpich.org > Cc: Lee, Eibhlin > Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem > > smpd was mainly meant for windows support. It is now deprecated, so we > don't officially support that. Someone on the mailing list might help, > but no promises. > > With respect to hydra, problems with that is what you should have > reported on this mailing list and we would have tried to help. :-) > > If ./main itself is not working, there's no hope of getting it to work > with mpiexec. You'll need to debug that first. > > -- Pavan > > On 06/13/2013 09:09 AM, Lee, Eibhlin wrote: >> Pavan, >> I had a lot of trouble getting hydra to work without having to enter a password/passphrase. I saw the option to pass a phrase in the mpich installers guide. I eventually found that for that command you needed to use the smpd process manager. That's the only reason I chose smpd over hydra. >> As to your other suggestion. I ran ./main and the same error (Can't open /dev/mem...) appeared. sudo ./main works but of course without multiple processes. >> Eibhlin >> ________________________________________ >> From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf of Pavan Balaji [balaji(a)mcs.anl.gov] >> Sent: 13 June 2013 14:34 >> To: discuss(a)mpich.org >> Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem >> >> I just saw your older email. Why are you using smpd instead of the >> default process manager (hydra)? >> >> -- Pavan >> >> On 06/13/2013 08:05 AM, Pavan Balaji wrote: >>> >>> What's "-phrase"? That's not a recognized option. I'm not sure where >>> the /dev/mem check is coming from. Try running ~/main without mpiexec >>> first. >>> >>> -- Pavan >>> >>> On 06/13/2013 06:56 AM, Lee, Eibhlin wrote: >>>> Hello all, >>>> >>>> I am trying to use two raspberry-pi to sample and then process some >>>> data. The first process samples while the second processes and vice >>>> versa. To do this I use gpio and also mpich-3.0.4 with the process >>>> manager smpd. I have successfully run cpi on both machines (from the >>>> master machine). I have also managed to run a similar program but >>>> without the MPI, this involved compiling with gcc and when running >>>> putting sudo in front of the binary file. >>>> >>>> When I combine these two processes I get various error messages. >>>> For input: >>>> mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>>> the error is: >>>> Can't open /dev/mem >>>> Did you forget to use 'sudo .. ?' >>>> >>>> For input: >>>> sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>>> the error is: >>>> sudo: mpiexec: Command not found >>>> >>>> I therefore put mpiexec into /usr/bin >>>> >>>> now for input: >>>> sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >>>> the error is: >>>> Can't open /dev/mem >>>> Did you forget to use 'sudo .. ?' >>>> >>>> Does anyone know how I can work around this? >>>> Thanks, >>>> Eibhlin >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >> _______________________________________________ >> 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 >> > > -- > Pavan Balaji > http://www.mcs.anl.gov/~balaji > -- Pavan Balaji http://www.mcs.anl.gov/~balaji

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