[OMPI users] MPI + system() call + Matlab MEX crashes

[juraj2...@gmail.com]

Hello,

I have an application in C++(main.cpp) that is launched with multiple
processes via mpirun. Master process calls matlab via system('matlab
-nosplash -nodisplay -nojvm -nodesktop -r "interface"'), which executes
simple script interface.m that calls mexFunction (mexsolve.cpp) from which
I try to set up communication with the rest of the processes launched at
the beginning together with the master process. When I run the application
as listed below on two different machines I experience:

1) crash at MPI_Init() in the mexFunction() on cluster machine with
Linux 4.4.0-22-generic

2) error in MPI_Send() shown below on local machine with
Linux 3.10.0-229.el7.x86_64
[archimedes:31962] shmem: mmap: an error occurred while determining whether
or not 
/tmp/openmpi-sessions-1007@archimedes_0/58444/1/shared_mem_pool.archimedes
could be created.
[archimedes:31962] create_and_attach: unable to create shared memory BTL
coordinating structure :: size 134217728
[archimedes:31962] shmem: mmap: an error occurred while determining whether
or not 
/tmp/openmpi-sessions-1007@archimedes_0/58444/1/0/vader_segment.archimedes.0
could be created.
[archimedes][[58444,1],0][../../../../../opal/mca/btl/tcp/
btl_tcp_endpoint.c:800:mca_btl_tcp_endpoint_complete_connect] connect() to
 failed: Connection refused (111)

I launch application as following:
mpirun --mca mpi_warn_on_fork 0 --mca btl_openib_want_fork_support 1  -np 2
-npernode 1 ./main

I have openmpi-2.0.1 configured with --prefix=${INSTALLDIR}
--enable-mpi-fortran=all --with-pmi --disable-dlopen

For more details, the code is here: https://github.com/goghino/matlabMpiC

Thanks for any suggestions!

Juraj
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Re: [OMPI users] MPI + system() call + Matlab MEX crashes

[Dmitry N. Mikushin]

Hi Juraj,

Although MPI infrastructure may technically support forking, it's known
that not all system resources can correctly replicate themselves to forked
process. For example, forking inside MPI program with active CUDA driver
will result into crash.

Why not to compile down the MATLAB into a native library and link it with
the MPI application directly? E.g. like here:
https://www.mathworks.com/matlabcentral/answers/98867-how-do-i-create-a-c-shared-library-from-mex-files-using-the-matlab-compiler?requestedDomain=www.mathworks.com

Kind regards,
- Dmitry Mikushin.


2016-10-05 11:32 GMT+03:00 juraj2...@gmail.com :

> Hello,
>
> I have an application in C++(main.cpp) that is launched with multiple
> processes via mpirun. Master process calls matlab via system('matlab
> -nosplash -nodisplay -nojvm -nodesktop -r "interface"'), which executes
> simple script interface.m that calls mexFunction (mexsolve.cpp) from which
> I try to set up communication with the rest of the processes launched at
> the beginning together with the master process. When I run the application
> as listed below on two different machines I experience:
>
> 1) crash at MPI_Init() in the mexFunction() on cluster machine with
> Linux 4.4.0-22-generic
>
> 2) error in MPI_Send() shown below on local machine with
> Linux 3.10.0-229.el7.x86_64
> [archimedes:31962] shmem: mmap: an error occurred while determining
> whether or not 
> /tmp/openmpi-sessions-1007@archimedes_0/58444/1/shared_mem_pool.archimedes
> could be created.
> [archimedes:31962] create_and_attach: unable to create shared memory BTL
> coordinating structure :: size 134217728
> [archimedes:31962] shmem: mmap: an error occurred while determining
> whether or not /tmp/openmpi-sessions-1007@arc
> himedes_0/58444/1/0/vader_segment.archimedes.0 could be created.
> [archimedes][[58444,1],0][../../../../../opal/mca/btl/tcp/bt
> l_tcp_endpoint.c:800:mca_btl_tcp_endpoint_complete_connect] connect() to
>  failed: Connection refused (111)
>
> I launch application as following:
> mpirun --mca mpi_warn_on_fork 0 --mca btl_openib_want_fork_support 1  -np
> 2 -npernode 1 ./main
>
> I have openmpi-2.0.1 configured with --prefix=${INSTALLDIR}
> --enable-mpi-fortran=all --with-pmi --disable-dlopen
>
> For more details, the code is here: https://github.com/goghino/matlabMpiC
>
> Thanks for any suggestions!
>
> Juraj
>
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Re: [OMPI users] Question on using Github to see bugs fixed in past versions

[Jeff Squyres (jsquyres)]

Additionally:

- When Open MPI migrated to github, we only brought over relevant open Trac 
tickets to Github.  As such, many old 1.10 and 1.8 (and earlier) issues were 
not brought over.
- Trac is still available in a read-only manner at 
https://svn.open-mpi.org/trac/ompi/report.


> On Oct 5, 2016, at 2:57 AM, Gilles Gouaillardet  wrote:
> 
> Edwin,
> 
> 
> 
> changes are summarized in the NEWS file
> 
> 
> 
> we used to have two github repositories, and they were "merged" recently
> 
> with github, you can list the closed PR for a given milestone
> 
> https://github.com/open-mpi/ompi-release/milestones?state=closed
> 
> then you can click on a milestone, and list the PR marked as "Closed"
> 
> for example, the PR merged in v1.10.4 are at 
> https://github.com/open-mpi/ompi-release/milestone/18?closed=1
> 
> 
> 
> Cheers,
> 
> 
> 
> Gilles
> 
> On 10/5/2016 5:10 AM, Blosch, Edwin L wrote:
>> Apologies for the dumb question… There used to be a way to dive in to see 
>> exactly what bugs and features came into 1.10.4, 1.10.3, and on back to 
>> 1.8.8.  Is there a way to do that on github?
>>  
>> Ed
>> 
> 
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[OMPI users] centos 7.2 openmpi from repo, stdout issue

[Emre Brookes]

$ cat /etc/redhat-release
CentOS Linux release 7.2.1511 (Core)

$ yum list installed | grep openmpi
openmpi.x86_64 1.10.0-10.el7   @base
openmpi-devel.x86_64   1.10.0-10.el7   @base

(1) When I run
$ mpirun -H myhosts -np myprocs executable
the job runs fine and outputs correctly to stdout

(2) When I run
$ mpirun -H myhosts -np myprocs executable > stdout.log
The stdout.log file prematurely ends (without full output)
... but the mpi executable itself seems to keep running forever until 
manually terminated will a "kill".


(3) When I run
$ mpirun -H myhosts -np myprocs executable | cat > stdout.log
the job runs fine and outputs correctly to the stdout.log file

I tried playing with a 'stdbuf' prefix to the command, but this didn't 
seem to help

I would like (2) to work, but have resorted to (3).

I tried digging around in the parameters after seeing 
https://github.com/open-mpi/ompi/issues/341
and thinking it might be something similar, but didn't see any poll or 
epoll in .conf
I am hesitant to try to compile from scratch and get away from the repo 
release cycle.


Is this a known bug?
If so, and if it has been fixed, would you recommend I install the 
latest stable rpm of 1.10.4-1 from 
https://www.open-mpi.org/software/ompi/v1.10/ ?


Thanks,
Emre






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[OMPI users] (no subject)

[Mahmood Naderan]

Hi,
Is there any idea about the following error? On that node, there are 15
empty cores.

Regards,
Mahmood
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[OMPI users] not enough slots available

[Mahmood Naderan]

Sorry about the incomplete message...

Is there any idea about the following error? On that node, there are 15
empty cores.

$ /share/apps/siesta/openmpi-2.0.1/bin/mpirun --host compute-0-3 -np 2
/share/apps/siesta/siesta-4.0-mpi201/tpar/transiesta < A.fdf
--
There are not enough slots available in the system to satisfy the 2 slots
that were requested by the application:
  /share/apps/siesta/siesta-4.0-mpi201/tpar/transiesta

Either request fewer slots for your application, or make more slots
available
for use.
--



Regards,
Mahmood
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Re: [OMPI users] not enough slots available

[Mahmood Naderan]

I found that if I put "compute-0-3" in a file (say hosts.txt) and pass that
file name via --hostfile, then the error disappears.

It is interesting to know what is the difference between these two? I think
it is very common to specify the nodes with --host option.


Regards,
Mahmood



On Wed, Oct 5, 2016 at 7:52 PM, Mahmood Naderan 
wrote:

> Sorry about the incomplete message...
>
> Is there any idea about the following error? On that node, there are 15
> empty cores.
>
> $ /share/apps/siesta/openmpi-2.0.1/bin/mpirun --host compute-0-3 -np 2
> /share/apps/siesta/siesta-4.0-mpi201/tpar/transiesta < A.fdf
> --
> There are not enough slots available in the system to satisfy the 2 slots
> that were requested by the application:
>   /share/apps/siesta/siesta-4.0-mpi201/tpar/transiesta
>
> Either request fewer slots for your application, or make more slots
> available
> for use.
> --
>
>
>
> Regards,
> Mahmood
>
>
>
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Re: [OMPI users] centos 7.2 openmpi from repo, stdout issue

[Jeff Squyres (jsquyres)]

We did have some kind of stdout/stderr truncation issue a little while ago, but 
I don't remember what version it specifically affected.

I would definitely update to at least Open MPI 1.10.4 (lots of bug fixes since 
1.10.0).  Better would be to update to Open MPI 2.0.1 -- that's the current 
generation and where all of our work is going these days.


> On Oct 5, 2016, at 9:23 AM, Emre Brookes  wrote:
> 
> $ cat /etc/redhat-release
> CentOS Linux release 7.2.1511 (Core)
> 
> $ yum list installed | grep openmpi
> openmpi.x86_64 1.10.0-10.el7   @base
> openmpi-devel.x86_64   1.10.0-10.el7   @base
> 
> (1) When I run
> $ mpirun -H myhosts -np myprocs executable
> the job runs fine and outputs correctly to stdout
> 
> (2) When I run
> $ mpirun -H myhosts -np myprocs executable > stdout.log
> The stdout.log file prematurely ends (without full output)
> ... but the mpi executable itself seems to keep running forever until 
> manually terminated will a "kill".
> 
> (3) When I run
> $ mpirun -H myhosts -np myprocs executable | cat > stdout.log
> the job runs fine and outputs correctly to the stdout.log file
> 
> I tried playing with a 'stdbuf' prefix to the command, but this didn't seem 
> to help
> I would like (2) to work, but have resorted to (3).
> 
> I tried digging around in the parameters after seeing 
> https://github.com/open-mpi/ompi/issues/341
> and thinking it might be something similar, but didn't see any poll or epoll 
> in .conf
> I am hesitant to try to compile from scratch and get away from the repo 
> release cycle.
> 
> Is this a known bug?
> If so, and if it has been fixed, would you recommend I install the latest 
> stable rpm of 1.10.4-1 from https://www.open-mpi.org/software/ompi/v1.10/ ?
> 
> Thanks,
> Emre
> 
> 
> 
> 
> 
> 
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Re: [OMPI users] centos 7.2 openmpi from repo, stdout issue

[Emre Brookes]

Thank you for the sanity check and recommendations.
I will post my results here when resolved.

Jeff Squyres (jsquyres) wrote:

We did have some kind of stdout/stderr truncation issue a little while ago, but 
I don't remember what version it specifically affected.

I would definitely update to at least Open MPI 1.10.4 (lots of bug fixes since 
1.10.0).  Better would be to update to Open MPI 2.0.1 -- that's the current 
generation and where all of our work is going these days.



On Oct 5, 2016, at 9:23 AM, Emre Brookes  wrote:

$ cat /etc/redhat-release
CentOS Linux release 7.2.1511 (Core)

$ yum list installed | grep openmpi
openmpi.x86_64 1.10.0-10.el7   @base
openmpi-devel.x86_64   1.10.0-10.el7   @base

(1) When I run
$ mpirun -H myhosts -np myprocs executable
the job runs fine and outputs correctly to stdout

(2) When I run
$ mpirun -H myhosts -np myprocs executable > stdout.log
The stdout.log file prematurely ends (without full output)
... but the mpi executable itself seems to keep running forever until manually terminated 
will a "kill".

(3) When I run
$ mpirun -H myhosts -np myprocs executable | cat > stdout.log
the job runs fine and outputs correctly to the stdout.log file

I tried playing with a 'stdbuf' prefix to the command, but this didn't seem to 
help
I would like (2) to work, but have resorted to (3).

I tried digging around in the parameters after seeing 
https://github.com/open-mpi/ompi/issues/341
and thinking it might be something similar, but didn't see any poll or epoll in 
.conf
I am hesitant to try to compile from scratch and get away from the repo release 
cycle.

Is this a known bug?
If so, and if it has been fixed, would you recommend I install the latest 
stable rpm of 1.10.4-1 from https://www.open-mpi.org/software/ompi/v1.10/ ?

Thanks,
Emre






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[OMPI users] openmpi and mpi4py compatibility

[Mahdi, Sam]

Hi everyone,

I had a quick question regarding the compatibility of openmpi and mpi4py. I
have openmpi 1.7.3 and mpi4py 1.3.1.  I know these are older versions of
each, but I was having some problems running a program that uses mpi4py and
openmpi, and I wanted to make sure it wasn't a compatibility issue between
the 2 versions of these programs.

Sincerely,
Sam
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Re: [OMPI users] openmpi and mpi4py compatibility

[Jason Maldonis]

Hi Sam,

I am not a developer but I am using mpi4py with openmpi-1.10.2.  For that
version, most of the functionality works, but I think there are some issues
with the mpi_spawn commands. Are you using the spawn commands?

I have no experience with the versions you are using, but I thought I'd
chime in just in case you ran into a similar issue as me.

Best,
Jason

Jason Maldonis
Research Assistant of Professor Paul Voyles
Materials Science Grad Student
University of Wisconsin, Madison
1509 University Ave, Rm 202
Madison, WI 53706
maldo...@wisc.edu

On Wed, Oct 5, 2016 at 2:29 PM, Mahdi, Sam 
wrote:

> Hi everyone,
>
> I had a quick question regarding the compatibility of openmpi and mpi4py.
> I have openmpi 1.7.3 and mpi4py 1.3.1.  I know these are older versions of
> each, but I was having some problems running a program that uses mpi4py and
> openmpi, and I wanted to make sure it wasn't a compatibility issue between
> the 2 versions of these programs.
>
> Sincerely,
> Sam
>
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Re: [OMPI users] openmpi and mpi4py compatibility

[Lisandro Dalcin]

On 5 October 2016 at 22:29, Mahdi, Sam  wrote:

> Hi everyone,
>
> I had a quick question regarding the compatibility of openmpi and mpi4py.
> I have openmpi 1.7.3 and mpi4py 1.3.1.  I know these are older versions of
> each, but I was having some problems running a program that uses mpi4py and
> openmpi, and I wanted to make sure it wasn't a compatibility issue between
> the 2 versions of these programs.
>
>
Hi, I'm the author of mpi4py. Could you elaborate on the issues you
experienced? I would start by disabling MPI_Init_threads() from mpi4py, for
you have to add the following code:

import mpi4py.rc
mpi4py.rc.threaded = False
from mpi4py import MPI

But you have to do it at the VERY BEGINNING of your code, more precisely,
the two first lines should be used before any attempt to "from mpi4py
import MPI".

PS: Any chance you can use a newer version of mpi4py, maybe even a git
checkout of the master branch?

-- 
Lisandro Dalcin

Research Scientist
Computer, Electrical and Mathematical Sciences & Engineering (CEMSE)
Extreme Computing Research Center (ECRC)
King Abdullah University of Science and Technology (KAUST)
http://ecrc.kaust.edu.sa/

4700 King Abdullah University of Science and Technology
al-Khawarizmi Bldg (Bldg 1), Office # 0109
Thuwal 23955-6900, Kingdom of Saudi Arabia
http://www.kaust.edu.sa

Office Phone: +966 12 808-0459
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Re: [OMPI users] MPI + system() call + Matlab MEX crashes

[Gilles Gouaillardet]

Juraj,


if i understand correctly, the "master" task calls MPI_Init(), and then 
fork&exec matlab.


In some cases (lack of hardware support), fork cannot even work. but 
let's assume it is fine for now.


Then, if i read between the lines, matlab calls mexFunction that MPI_Init().

As far as i am concerned, that cannot work.

The blocker is that a child cannot call MPI_Init() if its parent already 
called MPI_Init()



Fortunatly, you have some options :-)
1) start matlab from mpirun.
for example, if you want one master, two slaves and matlab, you can do 
something like

mpirun -np 1 master : -np 1 matlab : -np 2 slave

2) MPI_Comm_spawn matlab
master can MPI_Comm_spawn() matlab, and then matlab can merge the parent 
communicator,

and communicate to master and slaves

3) use the approach suggested by Dmitry
/* this is specific to matlab, and i have no experience with it */

One last point, MPI_Init() can be invoked only once per task
(e.g. if your mexFunction does
MPI_Init(); work(); MPI_Finalize();
then it can be invoked only once per mpirun

Cheers,

Gilles

On 10/5/2016 6:41 PM, Dmitry N. Mikushin wrote:

Hi Juraj,

Although MPI infrastructure may technically support forking, it's 
known that not all system resources can correctly replicate themselves 
to forked process. For example, forking inside MPI program with active 
CUDA driver will result into crash.


Why not to compile down the MATLAB into a native library and link it 
with the MPI application directly? E.g. like here: 
https://www.mathworks.com/matlabcentral/answers/98867-how-do-i-create-a-c-shared-library-from-mex-files-using-the-matlab-compiler?requestedDomain=www.mathworks.com


Kind regards,
- Dmitry Mikushin.


2016-10-05 11:32 GMT+03:00 juraj2...@gmail.com 
 >:


Hello,

I have an application in C++(main.cpp) that is launched with
multiple processes via mpirun. Master process calls matlab via
system('matlab -nosplash -nodisplay -nojvm -nodesktop -r
"interface"'), which executes simple script interface.m that calls
mexFunction (mexsolve.cpp) from which I try to set up
communication with the rest of the processes launched at the
beginning together with the master process. When I run the
application as listed below on two different machines I experience:

1) crash at MPI_Init() in the mexFunction() on cluster machine
with Linux 4.4.0-22-generic

2) error in MPI_Send() shown below on local machine with
Linux 3.10.0-229.el7.x86_64
[archimedes:31962] shmem: mmap: an error occurred while
determining whether or not
/tmp/openmpi-sessions-1007@archimedes_0/58444/1/shared_mem_pool.archimedes
could be created.
[archimedes:31962] create_and_attach: unable to create shared
memory BTL coordinating structure :: size 134217728
[archimedes:31962] shmem: mmap: an error occurred while
determining whether or not
/tmp/openmpi-sessions-1007@archimedes_0/58444/1/0/vader_segment.archimedes.0
could be created.

[archimedes][[58444,1],0][../../../../../opal/mca/btl/tcp/btl_tcp_endpoint.c:800:mca_btl_tcp_endpoint_complete_connect]
connect() to  failed: Connection refused (111)

I launch application as following:
mpirun --mca mpi_warn_on_fork 0 --mca btl_openib_want_fork_support
1  -np 2 -npernode 1 ./main

I have openmpi-2.0.1 configured with --prefix=${INSTALLDIR}
--enable-mpi-fortran=all --with-pmi --disable-dlopen

For more details, the code is here:
https://github.com/goghino/matlabMpiC


Thanks for any suggestions!

Juraj

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Re: [OMPI users] MPI + system() call + Matlab MEX crashes

[Bennet Fauber]

Matlab may have its own MPI installed.  It definitely does if you have
the parallel computing toolbox.  If you have that, it could be causing
problems.  If you can, you might consider compiling your Matlab
application into a standalone executable, then call that from your own
program.  That bypasses the Matlab user interface and may prove more
tractable  See the documentation for mcc if you have that.

http://www.mathworks.com/help/compiler/mcc.html

If you have that toolbox.

-- bennet


On Wed, Oct 5, 2016 at 8:03 PM, Gilles Gouaillardet  wrote:
> Juraj,
>
>
> if i understand correctly, the "master" task calls MPI_Init(), and then
> fork&exec matlab.
>
> In some cases (lack of hardware support), fork cannot even work. but let's
> assume it is fine for now.
>
> Then, if i read between the lines, matlab calls mexFunction that MPI_Init().
>
> As far as i am concerned, that cannot work.
>
> The blocker is that a child cannot call MPI_Init() if its parent already
> called MPI_Init()
>
>
> Fortunatly, you have some options :-)
> 1) start matlab from mpirun.
> for example, if you want one master, two slaves and matlab, you can do
> something like
> mpirun -np 1 master : -np 1 matlab : -np 2 slave
>
> 2) MPI_Comm_spawn matlab
> master can MPI_Comm_spawn() matlab, and then matlab can merge the parent
> communicator,
> and communicate to master and slaves
>
> 3) use the approach suggested by Dmitry
> /* this is specific to matlab, and i have no experience with it */
>
> One last point, MPI_Init() can be invoked only once per task
> (e.g. if your mexFunction does
> MPI_Init(); work(); MPI_Finalize();
> then it can be invoked only once per mpirun
>
> Cheers,
>
> Gilles
>
> On 10/5/2016 6:41 PM, Dmitry N. Mikushin wrote:
>
> Hi Juraj,
>
> Although MPI infrastructure may technically support forking, it's known that
> not all system resources can correctly replicate themselves to forked
> process. For example, forking inside MPI program with active CUDA driver
> will result into crash.
>
> Why not to compile down the MATLAB into a native library and link it with
> the MPI application directly? E.g. like here:
> https://www.mathworks.com/matlabcentral/answers/98867-how-do-i-create-a-c-shared-library-from-mex-files-using-the-matlab-compiler?requestedDomain=www.mathworks.com
>
> Kind regards,
> - Dmitry Mikushin.
>
>
> 2016-10-05 11:32 GMT+03:00 juraj2...@gmail.com :
>>
>> Hello,
>>
>> I have an application in C++(main.cpp) that is launched with multiple
>> processes via mpirun. Master process calls matlab via system('matlab
>> -nosplash -nodisplay -nojvm -nodesktop -r "interface"'), which executes
>> simple script interface.m that calls mexFunction (mexsolve.cpp) from which I
>> try to set up communication with the rest of the processes launched at the
>> beginning together with the master process. When I run the application as
>> listed below on two different machines I experience:
>>
>> 1) crash at MPI_Init() in the mexFunction() on cluster machine with Linux
>> 4.4.0-22-generic
>>
>> 2) error in MPI_Send() shown below on local machine with Linux
>> 3.10.0-229.el7.x86_64
>> [archimedes:31962] shmem: mmap: an error occurred while determining
>> whether or not
>> /tmp/openmpi-sessions-1007@archimedes_0/58444/1/shared_mem_pool.archimedes
>> could be created.
>> [archimedes:31962] create_and_attach: unable to create shared memory BTL
>> coordinating structure :: size 134217728
>> [archimedes:31962] shmem: mmap: an error occurred while determining
>> whether or not
>> /tmp/openmpi-sessions-1007@archimedes_0/58444/1/0/vader_segment.archimedes.0
>> could be created.
>>
>> [archimedes][[58444,1],0][../../../../../opal/mca/btl/tcp/btl_tcp_endpoint.c:800:mca_btl_tcp_endpoint_complete_connect]
>> connect() to  failed: Connection refused (111)
>>
>> I launch application as following:
>> mpirun --mca mpi_warn_on_fork 0 --mca btl_openib_want_fork_support 1  -np
>> 2 -npernode 1 ./main
>>
>> I have openmpi-2.0.1 configured with --prefix=${INSTALLDIR}
>> --enable-mpi-fortran=all --with-pmi --disable-dlopen
>>
>> For more details, the code is here: https://github.com/goghino/matlabMpiC
>>
>> Thanks for any suggestions!
>>
>> Juraj
>>
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