Re: [OMPI users] some mpi processes "disappear" on a cluster of servers

[John Hearns]

Apologies, I have not taken the time to read your comprehensive diagnostics!

As Gus says, this sounds like a memory problem.
My suspicion would be the kernel Out Of Memory (OOM) killer.
Log into those nodes (or ask your systems manager to do this). Look
closely at /var/log/messages where there will be notifications when
the OOM Killer kicks in and - well - kills large memory processes!
Grep for "killed process" in /var/log/messages

http://linux-mm.org/OOM_Killer

Re: [OMPI users] users Digest, Vol 2339, Issue 5

[Andrea Negri]

Hi, Gus and John,

my code (zeusmp2) is a F77 code ported in F95, and the very first time
I have launched it, the processed disappears almost immediately.
I checked the code with valgrind and some unallocated arrays were
passed wrongly to some subroutines.
After having corrected this bug, the code runs for a while and after
occour all the stuff described in my first post.
However, the code still performs a lot of main temporal cycle before
"die" (I don't know if thies piece of information is useful).

Now I'm going to check the memory usage, (I also have a lot of unused
variables in this pretty large code, maybe I shoud comment them).

uname -a returns
Linux cloud 2.6.9-42.0.3.ELsmp #1 SMP Thu Oct 5 16:29:37 CDT 2006
x86_64 x86_64 x86_64 GNU/Linux

ulimit -a returns:
core file size(blocks, -c) 0
data seg size   (kbytes, -d) unlimited
file size   (blocks, -f) unlimited
pending signals(-i) 1024
max locked memory (kbytes, -l) 32
max memory size(kbytes, -m) unlimited
open files   (-n) 1024
pipe size(512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
stack size   (kbytes, -s) 10240
cpu time (seconds, -t) unlimited
max user processes (-u) 36864
virtual memory   (kbytes, -v) unlimited
file locks(-x) unlimited


I can log on the logins nodes, but unfortunately the command ls
/var/log/messages return
acpid   cron.4  messages.3 secure.4
anaconda.logcupsmessages.4 spooler
anaconda.syslog dmesg   mpi_uninstall.log  spooler.1
anaconda.xlog   gdm pppspooler.2
audit   httpd   prelink.logspooler.3
boot.logitac_uninstall.log  rpmpkgsspooler.4
boot.log.1  lastlog rpmpkgs.1  vbox
boot.log.2  mailrpmpkgs.2  wtmp
boot.log.3  maillog rpmpkgs.3  wtmp.1
boot.log.4  maillog.1   rpmpkgs.4  Xorg.0.log
cmkl_install.logmaillog.2   samba  Xorg.0.log.old
cmkl_uninstall.log  maillog.3   scrollkeeper.log   yum.log
cronmaillog.4   secure yum.log.1
cron.1  messagessecure.1
cron.2  messages.1  secure.2
cron.3  messages.2  secure.3

so, the log should be in some of these files (I don't have read
permission on these files). I'll contact the admin for that.

2012/9/1  :
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> Today's Topics:
>
>1. Re: some mpi processes "disappear" on a cluster ofservers
>   (Gus Correa)
>
>
> --
>
> Message: 1
> Date: Fri, 31 Aug 2012 20:11:41 -0400
> From: Gus Correa 
> Subject: Re: [OMPI users] some mpi processes "disappear" on a cluster
> of  servers
> To: Open MPI Users 
> Message-ID: <504152bd.3000...@ldeo.columbia.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Andrea
>
> I would guess this is a memory problem.
> Do you know how much memory each node has?
> Do you know the memory that
> each MPI process in the CFD code requires?
> If the program starts swapping/paging into disk, because of
> low memory, those interesting things that you described can happen.
>
> I would login to the compute nodes and monitor the
> amount of memory being used with "top" right after the program
> starts to run.  If there is a pattern of which node tends to fail,
> track login to that fail-prone node and monitor it.
>
> Alternatively, if you cluster is running Ganglia,
> you can see the memory use graphically,
> in the Ganglia web page in a web browser.
>
> If your cluster
> doesn't allow direct user logins to compute nodes,
> you can ask the system administrator to do this for you.
>
> It may well be that the code has a memory leak, or that
> it has a memory request spike, which may not be caught by
> OpenMPI.
> [Jeff and Ralph will probably correct me soon for
> saying this, and I know the OpenMPI safeguards against
> process misbehavior are great, but ...]
>
> Anyway, we had several codes here that would make a node go south
> because of either type of memory problem, and subse

Re: [OMPI users] what is a "node"?

[Zbigniew Koza]

Hi,

I have one more question.
I wanted to experiment with processor affinity command-line options on my
ubuntu PC.
When I use OpenMPI compiled from sourecs a few weeks ago, mpirun returns
error messages.
However, the"official" OpenMPI installation on the same machine makes no
problem.
Does it mean there's a  bug in OpenMPI-current and I should report a bug?

===  1. OpneMPI version: 

mpirun -V
mpirun (Open MPI) 1.9a1r26880

Report bugs to http://www.open-mpi.org/community/help/


 2. mpirun "offending" command and error report: ===

zkoza@zbyszek:~$ mpirun -np 2 --bind-to-core -bycore --report-bindings
uptime
--
WARNING: a request was made to bind a process. While the system
supports binding the process itself, at least one node does NOT
support binding memory to the process location.

  Node:  zbyszek

This is a warning only; your job will continue, though performance may
be degraded.
--
--
mpirun was unable to find the specified executable file, and therefore
did not launch the job.  This error was first reported for process
rank 0; it may have occurred for other processes as well.

NOTE: A common cause for this error is misspelling a mpirun command
  line parameter option (remember that mpirun interprets the first
  unrecognized command line token as the executable).

Node:   zbyszek
Executable: -bycore
--
2 total processes failed to start


 3. the same mpirun command using standard MPI installation 

LD_LIBRARY_PATH=/usr/lib/openmpi /usr/bin/mpirun --path /usr/lib/openmpi
-np 2 --bind-to-core -bycore --report-bindings uptime
[zbyszek:03104] [[7637,0],0] odls:default:fork binding child [[7637,1],0]
to cpus 0001
[zbyszek:03104] [[7637,0],0] odls:default:fork binding child [[7637,1],1]
to cpus 0002
 12:25:51 up 21:27,  1 user,  load average: 0.00, 0.01, 0.05
 12:25:51 up 21:27,  1 user,  load average: 0.00, 0.01, 0.05


 4. version of standard OpenMPI ===

zkoza@zbyszek:~$ LD_LIBRARY_PATH=/usr/lib/openmpi /usr/bin/mpirun --path
/usr/lib/openmpi --version
mpirun (Open MPI) 1.4.3



Z Koza

Re: [OMPI users] what is a "node"?

[Ralph Castain]

You are using cmd line options that no longer exist in the 1.9 release - look 
at "mpirun -h" for the current list of options.

FWIW: in your example, the correct cmd line would be:

mpirun -np 2 --bind-to core -map-by core --report-bindings uptime

Note the space in "--bind-to core" and the "-map-by" option syntax. The warning 
means that we didn't find libnuma installed on your machine, so we cannot bind 
memory allocations (but can bind processes).

On Sep 1, 2012, at 3:41 AM, Zbigniew Koza  wrote:

> Hi, 
> 
> I have one more question.
> I wanted to experiment with processor affinity command-line options on my 
> ubuntu PC.
> When I use OpenMPI compiled from sourecs a few weeks ago, mpirun returns 
> error messages.
> However, the"official" OpenMPI installation on the same machine makes no 
> problem.
> Does it mean there's a  bug in OpenMPI-current and I should report a bug?
> 
> ===  1. OpneMPI version: 
> 
> mpirun -V
> mpirun (Open MPI) 1.9a1r26880
> 
> Report bugs to http://www.open-mpi.org/community/help/
> 
> 
>  2. mpirun "offending" command and error report: ===
> 
> zkoza@zbyszek:~$ mpirun -np 2 --bind-to-core -bycore --report-bindings uptime
> --
> WARNING: a request was made to bind a process. While the system
> supports binding the process itself, at least one node does NOT
> support binding memory to the process location.
> 
>   Node:  zbyszek
> 
> This is a warning only; your job will continue, though performance may
> be degraded.
> --
> --
> mpirun was unable to find the specified executable file, and therefore
> did not launch the job.  This error was first reported for process
> rank 0; it may have occurred for other processes as well.
> 
> NOTE: A common cause for this error is misspelling a mpirun command
>   line parameter option (remember that mpirun interprets the first
>   unrecognized command line token as the executable).
> 
> Node:   zbyszek
> Executable: -bycore
> --
> 2 total processes failed to start
> 
> 
>  3. the same mpirun command using standard MPI installation 
> 
> LD_LIBRARY_PATH=/usr/lib/openmpi /usr/bin/mpirun --path /usr/lib/openmpi -np 
> 2 --bind-to-core -bycore --report-bindings uptime
> [zbyszek:03104] [[7637,0],0] odls:default:fork binding child [[7637,1],0] to 
> cpus 0001
> [zbyszek:03104] [[7637,0],0] odls:default:fork binding child [[7637,1],1] to 
> cpus 0002
>  12:25:51 up 21:27,  1 user,  load average: 0.00, 0.01, 0.05
>  12:25:51 up 21:27,  1 user,  load average: 0.00, 0.01, 0.05
> 
> 
>  4. version of standard OpenMPI ===
> 
> zkoza@zbyszek:~$ LD_LIBRARY_PATH=/usr/lib/openmpi /usr/bin/mpirun --path 
> /usr/lib/openmpi --version
> mpirun (Open MPI) 1.4.3
> 
> 
> 
> Z Koza
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

Re: [OMPI users] what is a "node"?

[Zbigniew Koza]

Thanks, Ralph,

the new syntax works well (I used "man mpirun", which displayed the old
syntax).
Also, the report displayed by --report-binding is far more human-readable
than in previous versions of OpenMPI

Out of curiosity, and also to supress the warning, I installed the
libnuma-dev package with libnuma.so and libnuma.a libraries, but the
warning remains.
Does it mean I should recompile OpenMPI to get rid of this warning?

Z Koza



2012/9/1 Ralph Castain 

> You are using cmd line options that no longer exist in the 1.9 release -
> look at "mpirun -h" for the current list of options.
>
> FWIW: in your example, the correct cmd line would be:
>
> mpirun -np 2 --bind-to core -map-by core --report-bindings uptime
>
> Note the space in "--bind-to core" and the "-map-by" option syntax. The
> warning means that we didn't find libnuma installed on your machine, so we
> cannot bind memory allocations (but can bind processes).
>
> On Sep 1, 2012, at 3:41 AM, Zbigniew Koza  wrote:
>
> Hi,
>
> I have one more question.
> I wanted to experiment with processor affinity command-line options on my
> ubuntu PC.
> When I use OpenMPI compiled from sourecs a few weeks ago, mpirun returns
> error messages.
> However, the"official" OpenMPI installation on the same machine makes no
> problem.
> Does it mean there's a  bug in OpenMPI-current and I should report a bug?
>
> ===  1. OpneMPI version: 
>
> mpirun -V
> mpirun (Open MPI) 1.9a1r26880
>
> Report bugs to http://www.open-mpi.org/community/help/
>
>
>  2. mpirun "offending" command and error report: ===
>
> zkoza@zbyszek:~$ mpirun -np 2 --bind-to-core -bycore --report-bindings
> uptime
> --
> WARNING: a request was made to bind a process. While the system
> supports binding the process itself, at least one node does NOT
> support binding memory to the process location.
>
>   Node:  zbyszek
>
> This is a warning only; your job will continue, though performance may
> be degraded.
> --
> --
> mpirun was unable to find the specified executable file, and therefore
> did not launch the job.  This error was first reported for process
> rank 0; it may have occurred for other processes as well.
>
> NOTE: A common cause for this error is misspelling a mpirun command
>   line parameter option (remember that mpirun interprets the first
>   unrecognized command line token as the executable).
>
> Node:   zbyszek
> Executable: -bycore
> --
> 2 total processes failed to start
>
>
>  3. the same mpirun command using standard MPI installation 
>
> LD_LIBRARY_PATH=/usr/lib/openmpi /usr/bin/mpirun --path /usr/lib/openmpi
> -np 2 --bind-to-core -bycore --report-bindings uptime
> [zbyszek:03104] [[7637,0],0] odls:default:fork binding child [[7637,1],0]
> to cpus 0001
> [zbyszek:03104] [[7637,0],0] odls:default:fork binding child [[7637,1],1]
> to cpus 0002
>  12:25:51 up 21:27,  1 user,  load average: 0.00, 0.01, 0.05
>  12:25:51 up 21:27,  1 user,  load average: 0.00, 0.01, 0.05
>
>
>  4. version of standard OpenMPI ===
>
> zkoza@zbyszek:~$ LD_LIBRARY_PATH=/usr/lib/openmpi /usr/bin/mpirun --path
> /usr/lib/openmpi --version
> mpirun (Open MPI) 1.4.3
>
>
>
> Z Koza
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
>
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users
>

Re: [OMPI users] some mpi processes "disappear" on a cluster of servers

[Andrea Negri]

I have tried to run with a single process (i.e. the entire grid is
contained by one process) and the the command free -m on the compute
node returns

 total   used   free sharedbuffers cached
Mem:  3913   1540   2372  0 49   1234
-/+ buffers/cache:257   3656
Swap: 1983  0   1983


while top returns
top - 16:01:09 up 4 days,  5:56,  1 user,  load average: 0.53, 0.16, 0.10
Tasks:  63 total,   3 running,  60 sleeping,   0 stopped,   0 zombie
Cpu(s): 49.4% us,  0.7% sy,  0.0% ni, 49.9% id,  0.0% wa,  0.0% hi,  0.0% si
Mem:   4007720k total,  1577968k used,  2429752k free,50664k buffers
Swap:  2031608k total,0k used,  2031608k free,  1263844k cached

Re: [OMPI users] what is a "node"?

[Ralph Castain]

On Sep 1, 2012, at 4:33 AM, Zbigniew Koza  wrote:

> Thanks, Ralph, 
> 
> the new syntax works well (I used "man mpirun", which displayed the old 
> syntax).

Ouch - will have to fix that. Thx

> Also, the report displayed by --report-binding is far more human-readable 
> than in previous versions of OpenMPI
> 
> Out of curiosity, and also to supress the warning, I installed the 
> libnuma-dev package with libnuma.so and libnuma.a libraries, but the warning 
> remains. 
> Does it mean I should recompile OpenMPI to get rid of this warning? 

I'll have to let Jeff answer that one, but I should think not as it is 
dynamically loaded. For now, you can turn that warning off by adding

-mca hwloc_base_mem_bind_failure_action silent

Jeff is responsible for the length of that param :-)


> 
> Z Koza
> 
>  
> 
> 2012/9/1 Ralph Castain 
> You are using cmd line options that no longer exist in the 1.9 release - look 
> at "mpirun -h" for the current list of options.
> 
> FWIW: in your example, the correct cmd line would be:
> 
> mpirun -np 2 --bind-to core -map-by core --report-bindings uptime
> 
> Note the space in "--bind-to core" and the "-map-by" option syntax. The 
> warning means that we didn't find libnuma installed on your machine, so we 
> cannot bind memory allocations (but can bind processes).
> 
> On Sep 1, 2012, at 3:41 AM, Zbigniew Koza  wrote:
> 
>> Hi, 
>> 
>> I have one more question.
>> I wanted to experiment with processor affinity command-line options on my 
>> ubuntu PC.
>> When I use OpenMPI compiled from sourecs a few weeks ago, mpirun returns 
>> error messages.
>> However, the"official" OpenMPI installation on the same machine makes no 
>> problem.
>> Does it mean there's a  bug in OpenMPI-current and I should report a bug?
>> 
>> ===  1. OpneMPI version: 
>> 
>> mpirun -V
>> mpirun (Open MPI) 1.9a1r26880
>> 
>> Report bugs to http://www.open-mpi.org/community/help/
>> 
>> 
>>  2. mpirun "offending" command and error report: ===
>> 
>> zkoza@zbyszek:~$ mpirun -np 2 --bind-to-core -bycore --report-bindings uptime
>> --
>> WARNING: a request was made to bind a process. While the system
>> supports binding the process itself, at least one node does NOT
>> support binding memory to the process location.
>> 
>>   Node:  zbyszek
>> 
>> This is a warning only; your job will continue, though performance may
>> be degraded.
>> --
>> --
>> mpirun was unable to find the specified executable file, and therefore
>> did not launch the job.  This error was first reported for process
>> rank 0; it may have occurred for other processes as well.
>> 
>> NOTE: A common cause for this error is misspelling a mpirun command
>>   line parameter option (remember that mpirun interprets the first
>>   unrecognized command line token as the executable).
>> 
>> Node:   zbyszek
>> Executable: -bycore
>> --
>> 2 total processes failed to start
>> 
>> 
>>  3. the same mpirun command using standard MPI installation 
>> 
>> LD_LIBRARY_PATH=/usr/lib/openmpi /usr/bin/mpirun --path /usr/lib/openmpi -np 
>> 2 --bind-to-core -bycore --report-bindings uptime
>> [zbyszek:03104] [[7637,0],0] odls:default:fork binding child [[7637,1],0] to 
>> cpus 0001
>> [zbyszek:03104] [[7637,0],0] odls:default:fork binding child [[7637,1],1] to 
>> cpus 0002
>>  12:25:51 up 21:27,  1 user,  load average: 0.00, 0.01, 0.05
>>  12:25:51 up 21:27,  1 user,  load average: 0.00, 0.01, 0.05
>> 
>> 
>>  4. version of standard OpenMPI ===
>> 
>> zkoza@zbyszek:~$ LD_LIBRARY_PATH=/usr/lib/openmpi /usr/bin/mpirun --path 
>> /usr/lib/openmpi --version
>> mpirun (Open MPI) 1.4.3
>> 
>> 
>> 
>> Z Koza
>> ___
>> users mailing list
>> us...@open-mpi.org
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
> 
> 
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users
> 
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

[OMPI users] Error: argv0 not available

[Austin Baker]

All,

I am quite new to using Open MPI as it is required by programs that I 
use for research. While running a chemistry program through Terminal, I 
inadvertently hit enter after I tried to run the program over multiple 
processors and am now getting one of two errors when I try and run the programs 
that I need. I've seen a couple of help topics that are along the same lines, 
but I can't seem to find an actual solution.

When I just ran the MPI this is the error I got
Austins-iMac:man1 ABProds$ 
/Applications/OpenEye/arch/osx-10.7-x64/oedocking/3.0.0/mpi/bin/mpirun -np 3

--
Sorry!  You were supposed to get help about:
orterun:executable-not-specified
from the file:
  help-orterun.txt
But I couldn't find any file matching that name.  Sorry!

When I try and run other programs that I need this is the error:
Austins-iMac:man1 ABProds$ 
/Applications/OpenEye/arch/osx-10.7-x64/oedocking/3.0.0/mpi/bin/mpirun -np 3
 /Applications/arch/osx-10.7-x64/oedocking/3.0.0/fred -receptor 

   ~/Documents/Research2012/FredData/Fyn_TargetSite.oeb -dbase  
 
~/Documents/Research2012/FredData/Zinc1/TopScores/zinc_57078852.mo;2 -numposes 
1500

--
Sorry!  You were supposed to get help about:
argv0-not-accessible
from the file:
help-rmgr-base.txt
But I couldn't find any file matching that name.  Sorry!


Very much appreciated for the help


Austin Baker
as...@pitt.edu
Graduate Student
Department of Chemistry
University of Pittsburgh

Everything is Experimental

Re: [OMPI users] Error: argv0 not available

[Jeff Squyres (jsquyres)]

The root cause is that you didn't specify an executable to run.

However, we might have some help messages missing, too. What version of OMPI 
are you running?

Sent from my phone. No type good.

On Sep 1, 2012, at 12:22 PM, "Austin Baker" 
mailto:as...@pitt.edu>> wrote:

All,

I am quite new to using Open MPI as it is required by programs that I use for 
research. While running a chemistry program through Terminal, I inadvertently 
hit enter after I tried to run the program over multiple processors and am now 
getting one of two errors when I try and run the programs that I need. I've 
seen a couple of help topics that are along the same lines, but I can't seem to 
find an actual solution.

When I just ran the MPI this is the error I got
Austins-iMac:man1 ABProds$ 
/Applications/OpenEye/arch/osx-10.7-x64/oedocking/3.0.0/mpi/bin/mpirun -np 3
--
Sorry!  You were supposed to get help about:
orterun:executable-not-specified
from the file:
help-orterun.txt
But I couldn't find any file matching that name.  Sorry!

When I try and run other programs that I need this is the error:
Austins-iMac:man1 ABProds$ 
/Applications/OpenEye/arch/osx-10.7-x64/oedocking/3.0.0/mpi/bin/mpirun -np 3 
/Applications/arch/osx-10.7-x64/oedocking/3.0.0/fred -receptor   
~/Documents/Research2012/FredData/Fyn_TargetSite.oeb -dbase 
~/Documents/Research2012/FredData/Zinc1/TopScores/zinc_57078852.mo;2 -numposes 
1500
--
Sorry!  You were supposed to get help about:
argv0-not-accessible
from the file:
help-rmgr-base.txt
But I couldn't find any file matching that name.  Sorry!


Very much appreciated for the help


Austin Baker
as...@pitt.edu
Graduate Student
Department of Chemistry
University of Pittsburgh

Everything is Experimental

___
users mailing list
us...@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users

Re: [OMPI users] Error: argv0 not available

[Austin Baker]

I have the most current version installed. I tried that first.


Austin Baker
as...@pitt.edu
Graduate Student
Department of Chemistry
University of Pittsburgh

Everything is Experimental

On Sep 1, 2012, at 12:41 PM, Jeff Squyres (jsquyres) wrote:

> The root cause is that you didn't specify an executable to run. 
> 
> However, we might have some help messages missing, too. What version of OMPI 
> are you running?
> 
> Sent from my phone. No type good. 
> 
> On Sep 1, 2012, at 12:22 PM, "Austin Baker"  wrote:
> 
>> All,
>> 
>> I am quite new to using Open MPI as it is required by programs that I use 
>> for research. While running a chemistry program through Terminal, I 
>> inadvertently hit enter after I tried to run the program over multiple 
>> processors and am now getting one of two errors when I try and run the 
>> programs that I need. I've seen a couple of help topics that are along the 
>> same lines, but I can't seem to find an actual solution.
>> 
>> When I just ran the MPI this is the error I got
>> Austins-iMac:man1 ABProds$ 
>> /Applications/OpenEye/arch/osx-10.7-x64/oedocking/3.0.0/mpi/bin/mpirun -np 3
>> --
>> Sorry!  You were supposed to get help about:
>> orterun:executable-not-specified
>> from the file:
>> help-orterun.txt
>> But I couldn't find any file matching that name.  Sorry!
>> 
>> When I try and run other programs that I need this is the error:
>> Austins-iMac:man1 ABProds$ 
>> /Applications/OpenEye/arch/osx-10.7-x64/oedocking/3.0.0/mpi/bin/mpirun -np 3 
>> /Applications/arch/osx-10.7-x64/oedocking/3.0.0/fred -receptor   
>> ~/Documents/Research2012/FredData/Fyn_TargetSite.oeb -dbase 
>> ~/Documents/Research2012/FredData/Zinc1/TopScores/zinc_57078852.mo;2 
>> -numposes 1500
>> --
>> Sorry!  You were supposed to get help about:
>> argv0-not-accessible
>> from the file:
>> help-rmgr-base.txt
>> But I couldn't find any file matching that name.  Sorry!
>> 
>> 
>> Very much appreciated for the help
>> 
>> 
>> Austin Baker
>> as...@pitt.edu
>> Graduate Student
>> Department of Chemistry
>> University of Pittsburgh
>> 
>> Everything is Experimental
>> 
>> ___
>> users mailing list
>> us...@open-mpi.org
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

Re: [OMPI users] Error: argv0 not available

[Ralph Castain]

Current meaning 1.6.1, 1.9, 1.7,???

A simple "ompi_info" will tell you at the very top:
 
   Package: Open MPI rhc@Ralphs-iMac.local Distribution
Open MPI: 1.9a1r27207M
 

On Sep 1, 2012, at 10:10 AM, Austin Baker  wrote:

> I have the most current version installed. I tried that first.
> 
> 
> Austin Baker
> as...@pitt.edu
> Graduate Student
> Department of Chemistry
> University of Pittsburgh
> 
> Everything is Experimental
> 
> On Sep 1, 2012, at 12:41 PM, Jeff Squyres (jsquyres) wrote:
> 
>> The root cause is that you didn't specify an executable to run. 
>> 
>> However, we might have some help messages missing, too. What version of OMPI 
>> are you running?
>> 
>> Sent from my phone. No type good. 
>> 
>> On Sep 1, 2012, at 12:22 PM, "Austin Baker"  wrote:
>> 
>>> All,
>>> 
>>> I am quite new to using Open MPI as it is required by programs that I use 
>>> for research. While running a chemistry program through Terminal, I 
>>> inadvertently hit enter after I tried to run the program over multiple 
>>> processors and am now getting one of two errors when I try and run the 
>>> programs that I need. I've seen a couple of help topics that are along the 
>>> same lines, but I can't seem to find an actual solution.
>>> 
>>> When I just ran the MPI this is the error I got
>>> Austins-iMac:man1 ABProds$ 
>>> /Applications/OpenEye/arch/osx-10.7-x64/oedocking/3.0.0/mpi/bin/mpirun -np 3
>>> --
>>> Sorry!  You were supposed to get help about:
>>> orterun:executable-not-specified
>>> from the file:
>>> help-orterun.txt
>>> But I couldn't find any file matching that name.  Sorry!
>>> 
>>> When I try and run other programs that I need this is the error:
>>> Austins-iMac:man1 ABProds$ 
>>> /Applications/OpenEye/arch/osx-10.7-x64/oedocking/3.0.0/mpi/bin/mpirun -np 
>>> 3 /Applications/arch/osx-10.7-x64/oedocking/3.0.0/fred -receptor   
>>> ~/Documents/Research2012/FredData/Fyn_TargetSite.oeb -dbase 
>>> ~/Documents/Research2012/FredData/Zinc1/TopScores/zinc_57078852.mo;2 
>>> -numposes 1500
>>> --
>>> Sorry!  You were supposed to get help about:
>>> argv0-not-accessible
>>> from the file:
>>> help-rmgr-base.txt
>>> But I couldn't find any file matching that name.  Sorry!
>>> 
>>> 
>>> Very much appreciated for the help
>>> 
>>> 
>>> Austin Baker
>>> as...@pitt.edu
>>> Graduate Student
>>> Department of Chemistry
>>> University of Pittsburgh
>>> 
>>> Everything is Experimental
>>> 
>>> ___
>>> users mailing list
>>> us...@open-mpi.org
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>> ___
>> users mailing list
>> us...@open-mpi.org
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
> 
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

Re: [OMPI users] Error: argv0 not available

[Reuti]

Am 01.09.2012 um 18:20 schrieb Austin Baker:

> All,
> 
>   I am quite new to using Open MPI as it is required by programs that I 
> use for research. While running a chemistry program through Terminal, I 
> inadvertently hit enter after I tried to run the program over multiple 
> processors and am now getting one of two errors when I try and run the 
> programs that I need. I've seen a couple of help topics that are along the 
> same lines, but I can't seem to find an actual solution.
> 
> When I just ran the MPI this is the error I got
>   Austins-iMac:man1 ABProds$ 
> /Applications/OpenEye/arch/osx-10.7-x64/oedocking/3.0.0/mpi/bin/mpirun -np 3
>   
> --
>   Sorry!  You were supposed to get help about:
>   orterun:executable-not-specified
>   from the file:
> help-orterun.txt
>   But I couldn't find any file matching that name.  Sorry!

Was the Open MPI installation moved after compilation? You can try to define:

export OPAL_PREFIX=/Applications/OpenEye/arch/osx-10.7-x64/oedocking/3.0.0/mpi

to get a better error message.


> When I try and run other programs that I need this is the error:
>   Austins-iMac:man1 ABProds$ 
> /Applications/OpenEye/arch/osx-10.7-x64/oedocking/3.0.0/mpi/bin/mpirun -np 3  
>/Applications/arch/osx-10.7-x64/oedocking/3.0.0/fred -receptor 

Whatever "argv0-not-accessible" means - you missed "OpenEye" in the above line.


>   
>   ~/Documents/Research2012/FredData/Fyn_TargetSite.oeb -dbase 
>   
> ~/Documents/Research2012/FredData/Zinc1/TopScores/zinc_57078852.mo;2 
> -numposes 1500

Although a ";" is valid in a filename and can easily be entered in the Finder, 
it's necessary to escape it on the command line or put the complete argument in 
quotation marks.

As it's a commercial application, I would suggest to ask the vendor and/or use 
their forum/knowledgebase. Especially as they suggest to use their own wrapper 
`oempirun`.

-- Reuti


>   
> --
>   Sorry!  You were supposed to get help about:
>   argv0-not-accessible
>   from the file:
>   help-rmgr-base.txt
>   But I couldn't find any file matching that name.  Sorry!
> 
> 
> Very much appreciated for the help
> 
> 
> Austin Baker
> as...@pitt.edu
> Graduate Student
> Department of Chemistry
> University of Pittsburgh
> 
> Everything is Experimental
> 
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users