Charm++ parallel programming system

["Bennion, Brian" <Bennion1 AT llnl.gov>]

OK.  should have seen that one.
I get a little farther now....

 ../charmrun +p 12 ++mpiexec ++remote-shell mympiexec 
/g/g14/bennion1/g11Dir/NAMD_CVS-2011-08-29_Source/Linux-x86_64-ib-icc-sse3/namd2
 
/g/g14/bennion1/g11Dir/NAMD_CVS-2011-08-29_Source/Linux-x86_64-ib-icc-sse3/test/apoa1.namd
Charmrun> IBVERBS version of charmrun
This is dollar star -n 12 ./charmrun.32109
srun: Job is in held state, pending scheduler release
srun: job 1000777 queued and waiting for resources
srun: job 1000777 has been allocated resources
Charmrun> started all node programs in 7.786 seconds.
Charmrun: error on request socket--
Socket closed before recv.


________________________________________
From: Jim Phillips 
[jim AT ks.uiuc.edu]
Sent: Tuesday, September 06, 2011 3:28 PM
To: Bennion, Brian
Cc: 
charm AT cs.uiuc.edu
Subject: RE: [ppl] [charm] icc compiler option

You probably don't what the "shift; shift;" at the beginning, since it's
stripping off the "-n 12" arguments that I assume srun needs.

-Jim


On Tue, 6 Sep 2011, Bennion, Brian wrote:

> Hello Jim,
>
> OK this seems like its going to be painful.
> mpiexec doesn't exist on sierra.llnl.gov
>
> mympiexec file is below
> #!/bin/csh
> echo "This is dollar start "$*
> shift; shift; exec srun  $* -p pdebug
>
> when the command below is executed
>
> ../charmrun +p 12 ++mpiexec ++remote-shell mympiexec ../namd2 apoa1.namd
>
> The output is
>
> Charmrun> IBVERBS version of charmrun
> This is dollar star: -n 12 ./charmrun.24175
> srun: Job is in held state, pending scheduler release
> srun: job 1000773 queued and waiting for resources
> Charmrun> error 0 attaching to node:
> Timeout waiting for node-program to connect
>
> The charmrun.24175 file is script that seems to be hanging somewhere.  Its 
> contents are pasted below:
>
>
> #!/bin/sh
> Echo() {
>  echo 'Charmrun remote shell(127.0.0.1.0)>' $*
> }
> Exit() {
>  if [ $1 -ne 0 ]
>  then
>    Echo Exiting with error code $1
>  fi
>  exit $1
> }
> Find() {
>  loc=''
>  for dir in `echo $PATH | sed -e 's/:/ /g'`
>  do
>    test -f "$dir/$1" && loc="$dir/$1"
>  done
>  if [ "x$loc" = x ]
>  then
>    Echo $1 not found in your PATH "($PATH)"--
>    Echo set your path in your ~/.charmrunrc
>    Exit 1
>  fi
> }
> test -f "$HOME/.charmrunrc" && . "$HOME/.charmrunrc"
> DISPLAY='sierra0:16.0';export DISPLAY
> NETMAGIC="24175";export NETMAGIC
> CmiMyNode=$OMPI_COMM_WORLD_RANK
> test -z "$CmiMyNode" && CmiMyNode=$MPIRUN_RANK
> test -z "$CmiMyNode" && CmiMyNode=$PMI_RANK
> test -z "$CmiMyNode" && CmiMyNode=$PMI_ID
> test -z "$CmiMyNode" && (Echo Could not detect rank from environment ; Exit 
> 1)
> export CmiMyNode
> NETSTART="$CmiMyNode 192.168.112.1 48334 24175 0";export NETSTART
> CmiMyNodeSize='1'; export CmiMyNodeSize
> CmiMyForks='0'; export CmiMyForks
> CmiNumNodes=$OMPI_COMM_WORLD_SIZE
> test -z "$CmiNumNodes" && CmiNumNodes=$MPIRUN_NPROCS
> test -z "$CmiNumNodes" && CmiNumNodes=$PMI_SIZE
> test -z "$CmiNumNodes" && (Echo Could not detect node count from 
> environment ; Exit 1)
> export CmiNumNodes
> PATH="$PATH:/bin:/usr/bin:/usr/X/bin:/usr/X11/bin:/usr/local/bin:/usr/X11R6/bin:/usr/openwin/bin"
> if test ! -x 
> "/g/g11/NAMD_CVS-2011-08-29_Source/Linux-x86_64-ib-icc-sse3/tests/../namd2"
> then
>  Echo 'Cannot locate this node-program: 
> /g/g11/NAMD_CVS-2011-08-29_Source/Linux-x86_64-ib-icc-sse3/tests/../namd2'
>  Exit 1
> fi
> cd "/g/g11/NAMD_CVS-2011-08-29_Source/Linux-x86_64-ib-icc-sse3/tests"
> if test $? = 1
> then
>  Echo 'Cannot propagate this current directory:'
>  Echo '/g/g11/NAMD_CVS-2011-08-29_Source/Linux-x86_64-ib-icc-sse3/tests'
>  Exit 1
> fi
> rm -f /tmp/charmrun_err.$$
> ("/g/g11/NAMD_CVS-2011-08-29_Source/Linux-x86_64-ib-icc-sse3/tests/../namd2"
>   apoa1.namdq
> res=$?
> if [ $res -eq 127 ]
> then
>  (
>    
> "/g/g11/NAMD_CVS-2011-08-29_Source/Linux-x86_64-ib-icc-sse3/tests/../namd2"
>    ldd 
> "/g/g11/NAMD_CVS-2011-08-29_Source/Linux-x86_64-ib-icc-sse3/tests/../namd2"
>  ) > /tmp/charmrun_err.$$ 2>&1
> fi
> ) < /dev/null 1> /dev/null 2> /dev/null
> sleep 1
> if [ -r /tmp/charmrun_err.$$ ]
> then
>  cat /tmp/charmrun_err.$$
>  rm -f /tmp/charmrun_err.$$
>  Exit 1
> fi
> Exit 0
>
> From: Jim Phillips 
> [jim AT ks.uiuc.edu]
> Sent: Tuesday, September 06, 2011 2:22 PM
> To: Bennion, Brian
> Cc: 
> charm AT cs.uiuc.edu
> Subject: RE: [ppl] [charm] icc compiler option
>
> You use charmrun with the ++mpiexec option and a mympiexec script that
> runs your srun with whatever options it needs.  See this bit in notes.txt:
>
> -- Linux Clusters with InfiniBand or Other High-Performance Networks --
>
> Charm++ provides a special ibverbs network layer that uses InfiniBand
> networks directly through the OpenFabrics OFED ibverbs library.  This
> avoids efficiency and portability issues associated with MPI.  Look for
> pre-built ibverbs NAMD binaries or specify ibverbs when building Charm++.
>
> Writing batch job scripts to run charmrun in a queueing system can be
> challenging.  Since most clusters provide directions for using mpiexec
> to launch MPI jobs, charmrun provides a ++mpiexec option to use mpiexec
> to launch non-MPI binaries.  If "mpiexec -np <procs> ..." is not
> sufficient to launch jobs on your cluster you will need to write an
> executable mympiexec script like the following from TACC:
>
>   #!/bin/csh
>   shift; shift; exec ibrun $*
>
> The job is then launched (with full paths where needed) as:
>
>   charmrun +p<procs> ++mpiexec ++remote-shell mympiexec namd2 <configfile>
>
>
> -Jim
>
>
> On Tue, 6 Sep 2011, Bennion, Brian wrote:
>
>> Thanks for the patch.  It is a bit more sophisticated that what I would 
>> have come up with.
>>
>> How does one start an ibverbs namd2.8 executable when more than 1 node is 
>> needed.  With mpi builds I just tell our "srun" scheduler that I need 144 
>> tasks and it assigns the PEs appropriately.
>>
>> The same syntax only produced 144 separate but identical jobs.
>>
>> Brian
>>
>> ________________________________________
>> From: Jim Phillips 
>> [jim AT ks.uiuc.edu]
>> Sent: Tuesday, September 06, 2011 5:36 AM
>> To: Bennion, Brian
>> Cc: 
>> charm AT cs.uiuc.edu
>> Subject: RE: [ppl] [charm] icc compiler option
>>
>> Hi,
>>
>> The attached patch should fix this.
>>
>> -Jim
>>
>>
>> On Mon, 5 Sep 2011, Bennion, Brian wrote:
>>
>>> bennion1 35:~> icc -v
>>> icc version 12.1.0 (gcc version 4.1.2 compatibility)
>>> ld    /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/crt1.o 
>>> /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/crti.o 
>>> /usr/lib/gcc/x86_64-redhat-linux/4.1.2/crtbegin.o --eh-frame-hdr 
>>> -dynamic-linker /lib64/ld-linux-x86-64.so.2 
>>> -L/usr/local/tools/ifort-12.1.023-beta/lib -o a.out 
>>> -L/usr/local/tools/icc-12.1.023-beta/compiler/lib/intel64 
>>> -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 
>>> -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64 
>>> -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../.. -L/lib64 -L/lib 
>>> -L/usr/lib64 -L/usr/lib -rpath /usr/local/tools/icc-12.1.023-beta/lib 
>>> -rpath /usr/local/tools/ifort-12.1.023-beta/lib -Bstatic -limf -lsvml 
>>> -Bdynamic -lm -Bstatic -lipgo -ldecimal --as-needed -Bdynamic -lcilkrts 
>>> -lstdc++ --no-as-needed -lgcc -lgcc_s -Bstatic -lirc -Bdynamic -lc -lgcc 
>>> -lgcc_s -Bstatic -lirc_s -Bdynamic -ldl -lc 
>>> /usr/lib/gcc/x86_64-redhat-linux/4.1.2/crtend.o 
>>> /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/crtn.o
>>> /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/crt1.o: In 
>>> function `_start':
>>> (.text+0x20): undefined reference to `main'
>>>
>>> -----Original Message-----
>>> From: Jim Phillips 
>>> [mailto:jim AT ks.uiuc.edu]
>>> Sent: Saturday, September 03, 2011 1:32 PM
>>> To: Bennion, Brian
>>> Cc: 
>>> charm AT cs.uiuc.edu
>>> Subject: Re: [ppl] [charm] icc compiler option
>>>
>>>
>>> Actually, the Intel 12.x compilers use Version too:
>>>
>>> [jphillip@kidlogin2
>>>  ~]$ icc -v
>>> Version 12.0.4
>>>
>>> Brian, what does icc -v return for you?  On what platform?
>>>
>>> -Jim
>>>
>>>
>>> On Sat, 3 Sep 2011, Jim Phillips wrote:
>>>
>>>>
>>>> This must be new in the Intel 12.x compilers.
>>>>
>>>> What does "icc -v" look like for you?
>>>>
>>>> -Jim
>>>>
>>>>
>>>> On Fri, 2 Sep 2011, Bennion, Brian wrote:
>>>>
>>>>>
>>>>>
>>>>>
>>>>> Hello,
>>>>>
>>>>> In the charm632 version that I ships with namd2.8 there is a small bug 
>>>>> in
>>>>> the build scripts.  Specifically, if icc is requested as the compiler, 
>>>>> the
>>>>> build will fail because icc was not found.  In the cc-icc.sh script the
>>>>> grep command is looking for "Version"  all icc -v commands only show
>>>>> "version".
>>>>> The grep comand should have the "-i" option to check for both spellings.
>>>>>
>>>>> Brian
>>>>>
>>>>> _______________________________________________
>>>>> charm mailing list
>>>>> charm AT cs.uiuc.edu
>>>>> http://lists.cs.uiuc.edu/mailman/listinfo/charm
>>>>> _______________________________________________
>>>>> ppl mailing list
>>>>> ppl AT cs.uiuc.edu
>>>>> http://lists.cs.uiuc.edu/mailman/listinfo/ppl
>>>>>
>>>>
>>>
>>
>