July 2015 - discuss - mailman3.cels.anl.gov

Re: [mpich-discuss] hydra, stdin close(), and SLURM
by Aaron Knister 29 Jul '15

29 Jul '15

Thanks Pavan! -Aaron On 7/28/15 3:23 PM, Balaji, Pavan wrote: > Hi Aaron, > > I've committed it to mpich/master: > > http://git.mpich.org/mpich.git/commitdiff/6b41775b2056ff18b3c28aab71764e359… > > Thanks for the contribution. > > This should be in tonight's nightlies: > > http://www.mpich.org/static/downloads/nightly/master/mpich/ > > ... and in the upcoming mpich-3.2rc1 release. > > -- Pavan > > > > > On 7/27/15, 1:40 PM, "Balaji, Pavan" <balaji(a)anl.gov> wrote: > >> Hi Aaron, >> >> >> >> Please send the patch to me directly. >> >> General guidelines as to the kind of patches we ask for: >> >> https://wiki.mpich.org/mpich/index.php/Version_Control_Systems_101 >> >> You can ignore the git workflow related text, which is for our internal testing. I'll take care of that for you. >> >> Thanks, >> >> -- Pavan >> >> On 7/27/15, 1:36 PM, "Aaron Knister" <aaron.s.knister(a)nasa.gov> wrote: >> >>> Hi Pavan, >>> >>> I see your reply in the archives but it didn't make it to my inbox so >>> I'm replying to my post. I don't disagree without you about the error >>> being in the SLURM code, but I'm not sure how one would prevent this >>> reliably. SLURM has no expectation that an external library will open >>> something at file descriptor 0 before it reaches the point in the code >>> where it's ready to poll for stdin. Do you have any suggestions? >>> >>> It's been a long while since I've done a git e-mail patch so it might >>> take me a bit to figure out. Should I send the patch to the list or to >>> you directly? >>> >>> Thanks! >>> >>> -Aaron >>> >>> On 7/25/15 10:26 PM, Aaron Knister wrote: >>>> I sent this off to the mvapich list yesterday and it was suggested I >>>> raise it here since this is the upstream project: >>>> >>>> This is a bit of a cross post from a thread I started on the slurm dev >>>> list: http://article.gmane.org/gmane.comp.distributed.slurm.devel/8176 >>>> >>>> I'd like to get feedback on the idea that "--input none" be passed to >>>> srun when using the SLURM hydra bootstrap mechanism. I figured it >>>> would be inserted somewhere around here >>>> http://trac.mpich.org/projects/mpich/browser/src/pm/hydra/tools/bootstrap/e…. >>>> >>>> >>>> Without this argument I'm getting spurious job aborts and confusing >>>> errors. The gist of it is mpiexec.hydra closes stdin before it exec's >>>> srun. srun then (possibly via the munge libraries) calls some function >>>> that does a look up via nss. We use sssd for AAA so libnss_sssd will >>>> handle this request. Part of the caching mechanism sssd uses will >>>> cause the library to open() the cache file. The lowest fd available is >>>> 0 so the cache file is opened on fd 0. srun then believes it's got >>>> stdin attached and it causes the issues outlined in the slurm dev >>>> post. I think passing "--input none" is the right thing to do here >>>> since hydra has in fact closed stdin to srun. I tested this via the >>>> HYDRA_LAUNCHER_EXTRA_ARGS environment variable and it does resolve the >>>> errors I described. >>>> >>>> Thanks! >>>> -Aaron >>>> >>> -- >>> Aaron Knister >>> NASA Center for Climate Simulation (Code 606.2) >>> Goddard Space Flight Center >>> (301) 286-2776 >>> >>> >> _______________________________________________ >> 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 -- Aaron Knister NASA Center for Climate Simulation (Code 606.2) Goddard Space Flight Center (301) 286-2776 _______________________________________________ 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] PANFS Remove RAID0 and add RAIDN to MPICH 3.2
by Rob Latham 29 Jul '15

29 Jul '15

On 07/29/2015 07:07 AM, Victorelli, Ron wrote: > I am a developer at Panasas, and we would like to provide a patch that > > removes RAID0 support and adds RAIDN support to romio (MPICH 3.2): > > src/mpi/romio/adio/ad_panfs/ad_panfs_open.c > > I currently do not have an MCS or trac account. Hi Ron. I'm pleased to have contributions from Panasas. It's your first since 2007! If you've got a lot of patches in the works, maybe we should go ahead and set you up with a trac account and/or a git tree. If you're just looking to get this patch into the tree, that's fine too: it's definitely easier and you will just need to 'git format-patch' your changes and email them to me. ==rob > > Thank You > > Ron Victorelli > > Software Engineer > > Panasas, Inc > > Email: rvictorelli(a)panasas.com <mailto:[email protected]> > > Tel: 412 -323-6422 > > www.panasas.com <http://www.panasas.com> > > Panasas_Logo_LR > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > -- Rob Latham Mathematics and Computer Science Division Argonne National Lab, IL USA _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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PANFS Remove RAID0 and add RAIDN to MPICH 3.2
by Victorelli, Ron 29 Jul '15

29 Jul '15

I am a developer at Panasas, and we would like to provide a patch that removes RAID0 support and adds RAIDN support to romio (MPICH 3.2): src/mpi/romio/adio/ad_panfs/ad_panfs_open.c I currently do not have an MCS or trac account. Thank You Ron Victorelli Software Engineer Panasas, Inc Email: rvictorelli(a)panasas.com<mailto:[email protected]> Tel: 412 -323-6422 www.panasas.com<http://www.panasas.com> [Panasas_Logo_LR] _______________________________________________ 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] hydra, stdin close(), and SLURM
by Balaji, Pavan 28 Jul '15

28 Jul '15

Hi Aaron, I've committed it to mpich/master: http://git.mpich.org/mpich.git/commitdiff/6b41775b2056ff18b3c28aab71764e359… Thanks for the contribution. This should be in tonight's nightlies: http://www.mpich.org/static/downloads/nightly/master/mpich/ ... and in the upcoming mpich-3.2rc1 release. -- Pavan On 7/27/15, 1:40 PM, "Balaji, Pavan" <balaji(a)anl.gov> wrote: >Hi Aaron, > > > >Please send the patch to me directly. > >General guidelines as to the kind of patches we ask for: > > https://wiki.mpich.org/mpich/index.php/Version_Control_Systems_101 > >You can ignore the git workflow related text, which is for our internal testing. I'll take care of that for you. > >Thanks, > > -- Pavan > >On 7/27/15, 1:36 PM, "Aaron Knister" <aaron.s.knister(a)nasa.gov> wrote: > >>Hi Pavan, >> >>I see your reply in the archives but it didn't make it to my inbox so >>I'm replying to my post. I don't disagree without you about the error >>being in the SLURM code, but I'm not sure how one would prevent this >>reliably. SLURM has no expectation that an external library will open >>something at file descriptor 0 before it reaches the point in the code >>where it's ready to poll for stdin. Do you have any suggestions? >> >>It's been a long while since I've done a git e-mail patch so it might >>take me a bit to figure out. Should I send the patch to the list or to >>you directly? >> >>Thanks! >> >>-Aaron >> >>On 7/25/15 10:26 PM, Aaron Knister wrote: >>> I sent this off to the mvapich list yesterday and it was suggested I >>> raise it here since this is the upstream project: >>> >>> This is a bit of a cross post from a thread I started on the slurm dev >>> list: http://article.gmane.org/gmane.comp.distributed.slurm.devel/8176 >>> >>> I'd like to get feedback on the idea that "--input none" be passed to >>> srun when using the SLURM hydra bootstrap mechanism. I figured it >>> would be inserted somewhere around here >>> http://trac.mpich.org/projects/mpich/browser/src/pm/hydra/tools/bootstrap/e…. >>> >>> >>> Without this argument I'm getting spurious job aborts and confusing >>> errors. The gist of it is mpiexec.hydra closes stdin before it exec's >>> srun. srun then (possibly via the munge libraries) calls some function >>> that does a look up via nss. We use sssd for AAA so libnss_sssd will >>> handle this request. Part of the caching mechanism sssd uses will >>> cause the library to open() the cache file. The lowest fd available is >>> 0 so the cache file is opened on fd 0. srun then believes it's got >>> stdin attached and it causes the issues outlined in the slurm dev >>> post. I think passing "--input none" is the right thing to do here >>> since hydra has in fact closed stdin to srun. I tested this via the >>> HYDRA_LAUNCHER_EXTRA_ARGS environment variable and it does resolve the >>> errors I described. >>> >>> Thanks! >>> -Aaron >>> >> >>-- >>Aaron Knister >>NASA Center for Climate Simulation (Code 606.2) >>Goddard Space Flight Center >>(301) 286-2776 >> >> >_______________________________________________ >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] hydra, stdin close(), and SLURM
by Balaji, Pavan 27 Jul '15

27 Jul '15

Hi Aaron, Please send the patch to me directly. General guidelines as to the kind of patches we ask for: https://wiki.mpich.org/mpich/index.php/Version_Control_Systems_101 You can ignore the git workflow related text, which is for our internal testing. I'll take care of that for you. Thanks, -- Pavan On 7/27/15, 1:36 PM, "Aaron Knister" <aaron.s.knister(a)nasa.gov> wrote: >Hi Pavan, > >I see your reply in the archives but it didn't make it to my inbox so >I'm replying to my post. I don't disagree without you about the error >being in the SLURM code, but I'm not sure how one would prevent this >reliably. SLURM has no expectation that an external library will open >something at file descriptor 0 before it reaches the point in the code >where it's ready to poll for stdin. Do you have any suggestions? > >It's been a long while since I've done a git e-mail patch so it might >take me a bit to figure out. Should I send the patch to the list or to >you directly? > >Thanks! > >-Aaron > >On 7/25/15 10:26 PM, Aaron Knister wrote: >> I sent this off to the mvapich list yesterday and it was suggested I >> raise it here since this is the upstream project: >> >> This is a bit of a cross post from a thread I started on the slurm dev >> list: http://article.gmane.org/gmane.comp.distributed.slurm.devel/8176 >> >> I'd like to get feedback on the idea that "--input none" be passed to >> srun when using the SLURM hydra bootstrap mechanism. I figured it >> would be inserted somewhere around here >> http://trac.mpich.org/projects/mpich/browser/src/pm/hydra/tools/bootstrap/e…. >> >> >> Without this argument I'm getting spurious job aborts and confusing >> errors. The gist of it is mpiexec.hydra closes stdin before it exec's >> srun. srun then (possibly via the munge libraries) calls some function >> that does a look up via nss. We use sssd for AAA so libnss_sssd will >> handle this request. Part of the caching mechanism sssd uses will >> cause the library to open() the cache file. The lowest fd available is >> 0 so the cache file is opened on fd 0. srun then believes it's got >> stdin attached and it causes the issues outlined in the slurm dev >> post. I think passing "--input none" is the right thing to do here >> since hydra has in fact closed stdin to srun. I tested this via the >> HYDRA_LAUNCHER_EXTRA_ARGS environment variable and it does resolve the >> errors I described. >> >> Thanks! >> -Aaron >> > >-- >Aaron Knister >NASA Center for Climate Simulation (Code 606.2) >Goddard Space Flight Center >(301) 286-2776 > > _______________________________________________ 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] hydra, stdin close(), and SLURM
by Aaron Knister 27 Jul '15

27 Jul '15

Hi Pavan, I see your reply in the archives but it didn't make it to my inbox so I'm replying to my post. I don't disagree without you about the error being in the SLURM code, but I'm not sure how one would prevent this reliably. SLURM has no expectation that an external library will open something at file descriptor 0 before it reaches the point in the code where it's ready to poll for stdin. Do you have any suggestions? It's been a long while since I've done a git e-mail patch so it might take me a bit to figure out. Should I send the patch to the list or to you directly? Thanks! -Aaron On 7/25/15 10:26 PM, Aaron Knister wrote: > I sent this off to the mvapich list yesterday and it was suggested I > raise it here since this is the upstream project: > > This is a bit of a cross post from a thread I started on the slurm dev > list: http://article.gmane.org/gmane.comp.distributed.slurm.devel/8176 > > I'd like to get feedback on the idea that "--input none" be passed to > srun when using the SLURM hydra bootstrap mechanism. I figured it > would be inserted somewhere around here > http://trac.mpich.org/projects/mpich/browser/src/pm/hydra/tools/bootstrap/e…. > > > Without this argument I'm getting spurious job aborts and confusing > errors. The gist of it is mpiexec.hydra closes stdin before it exec's > srun. srun then (possibly via the munge libraries) calls some function > that does a look up via nss. We use sssd for AAA so libnss_sssd will > handle this request. Part of the caching mechanism sssd uses will > cause the library to open() the cache file. The lowest fd available is > 0 so the cache file is opened on fd 0. srun then believes it's got > stdin attached and it causes the issues outlined in the slurm dev > post. I think passing "--input none" is the right thing to do here > since hydra has in fact closed stdin to srun. I tested this via the > HYDRA_LAUNCHER_EXTRA_ARGS environment variable and it does resolve the > errors I described. > > Thanks! > -Aaron > -- Aaron Knister NASA Center for Climate Simulation (Code 606.2) Goddard Space Flight Center (301) 286-2776 _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Help: configure flags and dependencies installation for RegCM-4.4.5.5
by Dhirendra Kumar 27 Jul '15

27 Jul '15

Dear Friends, I am trying to compile mpich-3.1.3 from a source file on a linux cluster with 8 nodes with following features- [dkumar@weather ~]$ cat /proc/cpuinfo processor : 0 vendor_id : GenuineIntel cpu family : 6 model : 45 model name : Intel(R) Xeon(R) CPU E5-2609 0 @ 2.40GHz stepping : 7 cpu MHz : 1200.000 cache size : 10240 KB physical id : 0 siblings : 4 core id : 0 cpu cores : 4 apicid : 0 initial apicid : 0 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm dca sse4_1 sse4_2 x2apic popcnt aes xsave avx lahf_lm arat epb xsaveopt pln pts dts tpr_shadow vnmi flexpriority ept vpid bogomips : 4788.63 clflush size : 64 cache_alignment : 64 address sizes : 46 bits physical, 48 bits virtual power management: ...................................................................................... ....................................................................................... processor : 7 ....................................................................................... Please suggest me where to set the prefix, and other configure flags as I want to compile it for RegCM-4.4.5.5 to run in parallel mode using all the nodes. also if possible please suggest me how to proceed for the installation of the hdf5 and netcdf dependencies for parallel run of the RegCM. Any help would be appreciated. Thanks and Regards -- ======================================== Dhirendra Kumar UGC-JRF School of Environmental Sciences, JNU New Delhi (India) Contact: +91 9910778043 Alternate email: dhirendra.cub(a)outlook.com ========================================= _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] Error while building MPICH-3.1.4
by Balaji, Pavan 26 Jul '15

26 Jul '15

It looks like the timestamps are messed up (possibly because you untarred it on an shared file system with different time stamps for different machines). Can you try to do a fresh untar and rebuild? If that doesn't work, you can also trying passing the --disable-maintainer-mode configure option. -- Pavan From: Viswanath Krishnamurthy Reply-To: "discuss(a)mpich.org<mailto:[email protected]>" Date: Sunday, July 26, 2015 at 7:54 AM To: "discuss(a)mpich.org<mailto:[email protected]>" Subject: Re: [mpich-discuss] Error while building MPICH-3.1.4 Hi all, I am currently trying to install MPICH-3.1.4 version on Ubuntu 14.04.2 -LTS and am getting the following error. ( cd /home/viswa/libraries/mpich-3.1.4 && /home/viswa/libraries/mpich-3.1.4/maint/extractcvars --dirs="`cat /home/viswa/libraries/mpich-3.1.4/maint/cvardirs`") Error: open directory /tmp/axpzlRB5Gz/mpich-3.1.4/maint/../src/mpi -- No such file or directory make[2]: *** [/home/viswa/libraries/mpich-3.1.4/src/util/cvar/mpich_cvars.c] Error 2 make[2]: Leaving directory `/home/viswa/mpibuilddir' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/viswa/mpibuilddir' make: *** [all] Error 2 Have attached m.txt and c.txt after building MPICH using command Am I missing any packages here? Thanks, Viswanath _______________________________________________ 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] hydra, stdin close(), and SLURM
by Balaji, Pavan 26 Jul '15

26 Jul '15

Thanks, Aaron. That seems like a reasonable workaround (though the error is really in the slurm code for assuming that fd 0 is already stdin). Do you think you can provide a git patch? I can signoff on it (which is our way of "reviewing it") and include it in the upcoming release. Regards, -- Pavan On 7/25/15, 9:26 PM, "Aaron Knister" <aaron.s.knister(a)nasa.gov> wrote: >I sent this off to the mvapich list yesterday and it was suggested I >raise it here since this is the upstream project: > >This is a bit of a cross post from a thread I started on the slurm dev >list: http://article.gmane.org/gmane.comp.distributed.slurm.devel/8176 > >I'd like to get feedback on the idea that "--input none" be passed to >srun when using the SLURM hydra bootstrap mechanism. I figured it would >be inserted somewhere around here >http://trac.mpich.org/projects/mpich/browser/src/pm/hydra/tools/bootstrap/e…. > > >Without this argument I'm getting spurious job aborts and confusing >errors. The gist of it is mpiexec.hydra closes stdin before it exec's >srun. srun then (possibly via the munge libraries) calls some function >that does a look up via nss. We use sssd for AAA so libnss_sssd will >handle this request. Part of the caching mechanism sssd uses will cause >the library to open() the cache file. The lowest fd available is 0 so >the cache file is opened on fd 0. srun then believes it's got stdin >attached and it causes the issues outlined in the slurm dev post. I >think passing "--input none" is the right thing to do here since hydra >has in fact closed stdin to srun. I tested this via the >HYDRA_LAUNCHER_EXTRA_ARGS environment variable and it does resolve the >errors I described. > >Thanks! >-Aaron > >-- >Aaron Knister >NASA Center for Climate Simulation (Code 606.2) >Goddard Space Flight Center >(301) 286-2776 > > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] Error while building MPICH-3.1.4
by Viswanath Krishnamurthy 26 Jul '15

26 Jul '15

Hi all, I am currently trying to install MPICH-3.1.4 version on Ubuntu 14.04.2 -LTS and am getting the following error. ( cd /home/viswa/libraries/mpich-3.1.4 && /home/viswa/libraries/mpich-3.1.4/maint/extractcvars --dirs="`cat /home/viswa/libraries/mpich-3.1.4/maint/cvardirs`") Error: open directory /tmp/axpzlRB5Gz/mpich-3.1.4/maint/../src/mpi -- No such file or directory make[2]: *** [/home/viswa/libraries/mpich-3.1.4/src/util/cvar/mpich_cvars.c] Error 2 make[2]: Leaving directory `/home/viswa/mpibuilddir' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/viswa/mpibuilddir' make: *** [all] Error 2 Have attached m.txt and c.txt after building MPICH using command Am I missing any packages here? Thanks, Viswanath _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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