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Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem
by Pavan Balaji 16 Jun '13

16 Jun '13

On 06/16/2013 04:53 AM, Lee, Eibhlin wrote: > Antonio set up a ticket > http://trac.mpich.org/projects/mpich/ticket/1885 to check whether the > problem would still occur in hydra. Could you please run the test > provided there with hydra and see if it works? I've verified that it works correctly and resolved the ticket. Please only use hydra. -- Pavan -- 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 16 Jun '13

16 Jun '13

Pavan, Antonio set up a ticket http://trac.mpich.org/projects/mpich/ticket/1885 to check whether the problem would still occur in hydra. Could you please run the test provided there with hydra and see if it works? Thanks, Eibhlin ________________________________________ From: Pavan Balaji [balaji(a)mcs.anl.gov] Sent: 16 June 2013 02:25 To: Lee, Eibhlin Cc: discuss(a)mpich.org Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem I thought you moved to Hydra when we mentioned that smpd was not supported. With smpd, you are on your own. Sorry. -- Pavan On 06/15/2013 12:18 PM, Lee, Eibhlin wrote: > Pavan, > > Normally I start smpd when I'm the normal user. This time I did it in root. It then prompted me for a smpd phrase (This happened the first time I ever started it in normal user but the first time it had appeared in root.) The uid=0 now. > > However, when I try to execute the program now, in root, it just hangs. With no messages at all! I checked and the cpi example does work when in root. > > Eibhlin > ________________________________________ > From: Pavan Balaji [balaji(a)mcs.anl.gov] > Sent: 15 June 2013 17:02 > To: discuss(a)mpich.org > Cc: Lee, Eibhlin > Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem > > On 06/14/2013 04:43 PM, Lee, Eibhlin wrote: >> sorry when I do run mpiexec id the output is >> uid=1000(pi) gid=1000(pi) >> groups=1000(pi),4(adm),20(dialout),24(cdrom),27(sudo),29(audio),44(video),46(plugdev),60(games),100(users),105(netdev),999(input) > > This is the crux of the problem. Your application processes are being > launched as the regular user (uid=1000) instead of as root (uid=0). I > assume this is how you ran the program; can you confirm? > > /* Login as root */ > % su > > % mpiexec [whatever_options] id > > -- Pavan > > -- > 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 15 Jun '13

15 Jun '13

I thought you moved to Hydra when we mentioned that smpd was not supported. With smpd, you are on your own. Sorry. -- Pavan On 06/15/2013 12:18 PM, Lee, Eibhlin wrote: > Pavan, > > Normally I start smpd when I'm the normal user. This time I did it in root. It then prompted me for a smpd phrase (This happened the first time I ever started it in normal user but the first time it had appeared in root.) The uid=0 now. > > However, when I try to execute the program now, in root, it just hangs. With no messages at all! I checked and the cpi example does work when in root. > > Eibhlin > ________________________________________ > From: Pavan Balaji [balaji(a)mcs.anl.gov] > Sent: 15 June 2013 17:02 > To: discuss(a)mpich.org > Cc: Lee, Eibhlin > Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem > > On 06/14/2013 04:43 PM, Lee, Eibhlin wrote: >> sorry when I do run mpiexec id the output is >> uid=1000(pi) gid=1000(pi) >> groups=1000(pi),4(adm),20(dialout),24(cdrom),27(sudo),29(audio),44(video),46(plugdev),60(games),100(users),105(netdev),999(input) > > This is the crux of the problem. Your application processes are being > launched as the regular user (uid=1000) instead of as root (uid=0). I > assume this is how you ran the program; can you confirm? > > /* Login as root */ > % su > > % mpiexec [whatever_options] id > > -- Pavan > > -- > Pavan Balaji > http://www.mcs.anl.gov/~balaji > -- Pavan Balaji http://www.mcs.anl.gov/~balaji

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Re: [mpich-discuss] MPI server setup issue
by Sufeng Niu 15 Jun '13

15 Jun '13

Hi, Antonio Thanks a lot for your reply. I run my program on 64 bit OS for each nodes. Do you know how can overcome this OS problems? Should I add compile flags as mpicc -m64 ....? Thanks a lot! Sufeng On Sat, Jun 15, 2013 at 10:03 AM, <discuss-request(a)mpich.org> wrote: > Send discuss mailing list submissions to > discuss(a)mpich.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.mpich.org/mailman/listinfo/discuss > or, via email, send a message with subject or body 'help' to > discuss-request(a)mpich.org > > You can reach the person managing the list at > discuss-owner(a)mpich.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of discuss digest..." > > > Today's Topics: > > 1. Re: MPI server setup issue (Antonio J. Pe?a) > 2. Re: Running an mpi program that needs to access /dev/mem > (Jim Dinan) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 14 Jun 2013 16:46:20 -0500 > From: Antonio J. Pe?a <apenya(a)mcs.anl.gov> > To: discuss(a)mpich.org > Subject: Re: [mpich-discuss] MPI server setup issue > Message-ID: <3198378.OIJ6uL42Ef(a)localhost.localdomain> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi Sufeng, > > > > On Friday, June 14, 2013 04:35:39 PM Sufeng Niu wrote: > > > > Hello, > > > > > > I am a beginner on MPI programming, and right now I am working on an > MPI project. I got a few questions related to implementation issues: > > > > > > 1. when I run a simple MPI hello world on multiple nodes, (I already > installed mpich3 library on master node, mount the nfs, shared the > executable file and mpi library, set slave node to be keyless ssh), my > program was stoped there say: > > bash: /mnt/mpi/mpich-install/bin/hydra_pmi_proxy: /lib/ld-linux.so.2: bad > ELF interpreter: No such file or directory. > > I can not get rid of it for a long times. even though I reset everything > (I > already add PATH=/mnt/mpi/mpich-install/bin:$PATH in .bash_profile). Do > you have any clues on this problems? > > > > > This issue may be related to mismatch between 32 and 64 bit libraries. Are > you running 64 or 32 bit operating systems in all of your nodes > consistently? > > > 2. for multiple servers, each of them has 10G ethernet card. for > example, one network card address is eth5: 10.0.5.55. So if I want to > launch MPI communication through 10G network card. Should I set the > hostfile as: 10.0.5.55:$(PROCESS_NUM)? Or using iface eth5 > > > You can address those nodes by either IP or DNS name in the hostfile, > depending on how your system is configured. Using IP addresses is > completely OK. > > > Best, > Antonio > > > > > > > Thanks a lot! > > > > > > -- Best Regards, > > Sufeng Niu > > ECASP lab, ECE department, Illinois Institute of Technology > > Tel: 312-731-7219 > > > > > >

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Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem
by Lee, Eibhlin 15 Jun '13

15 Jun '13

Jim, At the time I was checking it would run on one machine so I only changed it on the one machine I was running the program on. Eibhlin ________________________________ From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf of Jim Dinan [james.dinan(a)gmail.com] Sent: 15 June 2013 16:03 To: discuss(a)mpich.org Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem Eibhlin, Did you make those permissions changes on every node where your program runs? What happens if you run "mpiexec touch /dev/mem"? ~Jim. On Fri, Jun 14, 2013 at 4:43 PM, Lee, Eibhlin <eibhlin.lee10(a)imperial.ac.uk<mailto:[email protected]>> wrote: Pavan, sorry when I do run mpiexec id the output is uid=1000(pi) gid=1000(pi) groups=1000(pi),4(adm),20(dialout),24(cdrom),27(sudo),29(audio),44(video),46(plugdev),60(games),100(users),105(netdev),999(input) regardless of whether I'm in root or my usual user. root@raspi or pi@raspi. Is this output what you would expect? Jim, I have tried changing the ownership of /dev/mem by chmod 755 /dev/mem so that the output of ls -l /dev/mem is crwxr-xr-x 1 root kmem 1, 1 Jan 1 1970 /dev/mem but I still can't open /dev/mem inside my program. I also tried with the code 777. I tried adding my user to the kmem group by doing usermod -a -G kmem pi but this doesn't fix the problem. Have I gotten totally confused and pi isn't my user? Thank you in advance, Eibhlin ________________________________ From: discuss-bounces(a)mpich.org<mailto:[email protected]> [discuss-bounces(a)mpich.org<mailto:[email protected]>] on behalf of Jim Dinan [james.dinan(a)gmail.com<mailto:[email protected]>] Sent: 14 June 2013 21:31 To: discuss(a)mpich.org<mailto:[email protected]> Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem I don't know if this has been suggested, but you could also add your user to the kmem group and chmod /dev/mem so that you have the access you need. ~Jim. On Fri, Jun 14, 2013 at 1:24 PM, Pavan Balaji <balaji(a)mcs.anl.gov<mailto:[email protected]>> wrote: You can run mpich as root. There's no restriction on that. You still haven't tried out my suggestion of running "id" to check what user ID you are running your processes as. My guess is that you are not setting your user ID correctly. -- Pavan On 06/14/2013 06:27 AM, Lee, Eibhlin wrote: I found that the reason we want to access /dev/mem is to setup memory regions to access the peripherals. (We are trying to read the output of an ADC). At this point it becomes more a linux/raspberry-pi specific problem than an MPICH problem. Although the fact that you can't run a program that needs access to memory mapping (even as the root user) seems something that MPICH could improve on for future versions. I know I am using smpd instead of hydra so this problem may already be solved. But if someone could confirm that, it would be really helpful. ________________________________________ From: discuss-bounces(a)mpich.org<mailto:[email protected]> [discuss-bounces(a)mpich.org<mailto:[email protected]>] on behalf of Lee, Eibhlin [eibhlin.lee10(a)imperial.ac.uk<mailto:[email protected]>] Sent: 14 June 2013 11:20 To: discuss(a)mpich.org<mailto:[email protected]> Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem 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<mailto:[email protected]> [discuss-bounces(a)mpich.org<mailto:[email protected]>] on behalf of Gus Correa [gus(a)ldeo.columbia.edu<mailto:[email protected]>] 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<mailto:[email protected]> [discuss-bounces(a)mpich.org<mailto:[email protected]>] on behalf of Gus Correa [gus(a)ldeo.columbia.edu<mailto:[email protected]>] 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<mailto:[email protected]> [discuss-bounces(a)mpich.org<mailto:[email protected]>] on behalf of Pavan Balaji [balaji(a)mcs.anl.gov<mailto:[email protected]>] Sent: 13 June 2013 14:34 To: discuss(a)mpich.org<mailto:[email protected]> 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<mailto:[email protected]> 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<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<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<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<mailto:[email protected]> 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<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

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Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem
by Lee, Eibhlin 15 Jun '13

15 Jun '13

Pavan, Normally I start smpd when I'm the normal user. This time I did it in root. It then prompted me for a smpd phrase (This happened the first time I ever started it in normal user but the first time it had appeared in root.) The uid=0 now. However, when I try to execute the program now, in root, it just hangs. With no messages at all! I checked and the cpi example does work when in root. Eibhlin ________________________________________ From: Pavan Balaji [balaji(a)mcs.anl.gov] Sent: 15 June 2013 17:02 To: discuss(a)mpich.org Cc: Lee, Eibhlin Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem On 06/14/2013 04:43 PM, Lee, Eibhlin wrote: > sorry when I do run mpiexec id the output is > uid=1000(pi) gid=1000(pi) > groups=1000(pi),4(adm),20(dialout),24(cdrom),27(sudo),29(audio),44(video),46(plugdev),60(games),100(users),105(netdev),999(input) This is the crux of the problem. Your application processes are being launched as the regular user (uid=1000) instead of as root (uid=0). I assume this is how you ran the program; can you confirm? /* Login as root */ % su % mpiexec [whatever_options] id -- Pavan -- 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 15 Jun '13

15 Jun '13

On 06/14/2013 04:43 PM, Lee, Eibhlin wrote: > sorry when I do run mpiexec id the output is > uid=1000(pi) gid=1000(pi) > groups=1000(pi),4(adm),20(dialout),24(cdrom),27(sudo),29(audio),44(video),46(plugdev),60(games),100(users),105(netdev),999(input) This is the crux of the problem. Your application processes are being launched as the regular user (uid=1000) instead of as root (uid=0). I assume this is how you ran the program; can you confirm? /* Login as root */ % su % mpiexec [whatever_options] id -- Pavan -- 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 Jim Dinan 15 Jun '13

15 Jun '13

Eibhlin, Did you make those permissions changes on every node where your program runs? What happens if you run "mpiexec touch /dev/mem"? ~Jim. On Fri, Jun 14, 2013 at 4:43 PM, Lee, Eibhlin <eibhlin.lee10(a)imperial.ac.uk>wrote: > Pavan, > sorry when I do run mpiexec id the output is > uid=1000(pi) gid=1000(pi) > groups=1000(pi),4(adm),20(dialout),24(cdrom),27(sudo),29(audio),44(video),46(plugdev),60(games),100(users),105(netdev),999(input) > > regardless of whether I'm in root or my usual user. root@raspi or > pi@raspi. Is this output what you would expect? > > Jim, > I have tried changing the ownership of /dev/mem by > chmod 755 /dev/mem so that the output of ls -l /dev/mem is > crwxr-xr-x 1 root kmem 1, 1 Jan 1 1970 /dev/mem > but I still can't open /dev/mem inside my program. I also tried with the > code 777. > > I tried adding my user to the kmem group by doing > usermod -a -G kmem pi > but this doesn't fix the problem. > > > Have I gotten totally confused and pi isn't my user? > > Thank you in advance, > Eibhlin > ------------------------------ > *From:* discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf > of Jim Dinan [james.dinan(a)gmail.com] > *Sent:* 14 June 2013 21:31 > > *To:* discuss(a)mpich.org > *Subject:* Re: [mpich-discuss] Running an mpi program that needs to > access /dev/mem > > I don't know if this has been suggested, but you could also add your > user to the kmem group and chmod /dev/mem so that you have the access you > need. > > ~Jim. > > > On Fri, Jun 14, 2013 at 1:24 PM, Pavan Balaji <balaji(a)mcs.anl.gov> wrote: > >> >> You can run mpich as root. There's no restriction on that. You still >> haven't tried out my suggestion of running "id" to check what user ID you >> are running your processes as. My guess is that you are not setting your >> user ID correctly. >> >> -- Pavan >> >> >> On 06/14/2013 06:27 AM, Lee, Eibhlin wrote: >> >>> I found that the reason we want to access /dev/mem is to setup memory >>> regions to access the peripherals. (We are trying to read the output of an >>> ADC). At this point it becomes more a linux/raspberry-pi specific problem >>> than an MPICH problem. Although the fact that you can't run a program that >>> needs access to memory mapping (even as the root user) seems something that >>> MPICH could improve on for future versions. I know I am using smpd instead >>> of hydra so this problem may already be solved. But if someone could >>> confirm that, it would be really helpful. >>> ______________________________**__________ >>> From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf >>> of Lee, Eibhlin [eibhlin.lee10(a)imperial.ac.uk] >>> Sent: 14 June 2013 11:20 >>> To: discuss(a)mpich.org >>> Subject: Re: [mpich-discuss] Running an mpi program that needs >>> to access /dev/mem >>> >>> 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<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<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<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<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<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<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<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<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<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] MPI server setup issue
by Antonio J. Peña 14 Jun '13

14 Jun '13

Hi Sufeng, > On Friday, June 14, 2013 04:35:39 PM Sufeng Niu wrote: > Hello, > > I am a beginner on MPI programming, and right now I am working on an MPI project. I got a few questions related to implementation issues: > > 1. when I run a simple MPI hello world on multiple nodes, (I already installed mpich3 library on master node, mount the nfs, shared the executable file and mpi library, set slave node to be keyless ssh), my program was stoped there say: > bash: /mnt/mpi/mpich-install/bin/hydra_pmi_proxy: /lib/ld-linux.so.2: bad ELF interpreter: No such file or directory. > I can not get rid of it for a long times. even though I reset everything (I already add PATH=/mnt/mpi/mpich-install/bin:$PATH in .bash_profile). Do you have any clues on this problems? > This issue may be related to mismatch between 32 and 64 bit libraries. Are you running 64 or 32 bit operating systems in all of your nodes consistently? > 2. for multiple servers, each of them has 10G ethernet card. for example, one network card address is eth5: 10.0.5.55. So if I want to launch MPI communication through 10G network card. Should I set the hostfile as: 10.0.5.55:$(PROCESS_NUM)? Or using iface eth5 You can address those nodes by either IP or DNS name in the hostfile, depending on how your system is configured. Using IP addresses is completely OK. Best, Antonio > > Thanks a lot! > > -- Best Regards, > Sufeng Niu > ECASP lab, ECE department, Illinois Institute of Technology > Tel: 312-731-7219 >

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

14 Jun '13

Pavan, sorry when I do run mpiexec id the output is uid=1000(pi) gid=1000(pi) groups=1000(pi),4(adm),20(dialout),24(cdrom),27(sudo),29(audio),44(video),46(plugdev),60(games),100(users),105(netdev),999(input) regardless of whether I'm in root or my usual user. root@raspi or pi@raspi. Is this output what you would expect? Jim, I have tried changing the ownership of /dev/mem by chmod 755 /dev/mem so that the output of ls -l /dev/mem is crwxr-xr-x 1 root kmem 1, 1 Jan 1 1970 /dev/mem but I still can't open /dev/mem inside my program. I also tried with the code 777. I tried adding my user to the kmem group by doing usermod -a -G kmem pi but this doesn't fix the problem. Have I gotten totally confused and pi isn't my user? Thank you in advance, Eibhlin ________________________________ From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf of Jim Dinan [james.dinan(a)gmail.com] Sent: 14 June 2013 21:31 To: discuss(a)mpich.org Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem I don't know if this has been suggested, but you could also add your user to the kmem group and chmod /dev/mem so that you have the access you need. ~Jim. On Fri, Jun 14, 2013 at 1:24 PM, Pavan Balaji <balaji(a)mcs.anl.gov<mailto:[email protected]>> wrote: You can run mpich as root. There's no restriction on that. You still haven't tried out my suggestion of running "id" to check what user ID you are running your processes as. My guess is that you are not setting your user ID correctly. -- Pavan On 06/14/2013 06:27 AM, Lee, Eibhlin wrote: I found that the reason we want to access /dev/mem is to setup memory regions to access the peripherals. (We are trying to read the output of an ADC). At this point it becomes more a linux/raspberry-pi specific problem than an MPICH problem. Although the fact that you can't run a program that needs access to memory mapping (even as the root user) seems something that MPICH could improve on for future versions. I know I am using smpd instead of hydra so this problem may already be solved. But if someone could confirm that, it would be really helpful. ________________________________________ From: discuss-bounces(a)mpich.org<mailto:[email protected]> [discuss-bounces(a)mpich.org<mailto:[email protected]>] on behalf of Lee, Eibhlin [eibhlin.lee10(a)imperial.ac.uk<mailto:[email protected]>] Sent: 14 June 2013 11:20 To: discuss(a)mpich.org<mailto:[email protected]> Subject: Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem 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<mailto:[email protected]> [discuss-bounces(a)mpich.org<mailto:[email protected]>] on behalf of Gus Correa [gus(a)ldeo.columbia.edu<mailto:[email protected]>] 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<mailto:[email protected]> [discuss-bounces(a)mpich.org<mailto:[email protected]>] on behalf of Gus Correa [gus(a)ldeo.columbia.edu<mailto:[email protected]>] 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<mailto:[email protected]> [discuss-bounces(a)mpich.org<mailto:[email protected]>] on behalf of Pavan Balaji [balaji(a)mcs.anl.gov<mailto:[email protected]>] Sent: 13 June 2013 14:34 To: discuss(a)mpich.org<mailto:[email protected]> 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<mailto:[email protected]> 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<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<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<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<mailto:[email protected]> 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<mailto:[email protected]> To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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