[mpi4py] demo/helloworld.py errors

[Dongting]

Hello,

I installed mpi4py locally (to $HOME) and it seems Python can import
mpi4py as a module. However, when I try to run the test program
helloworld.py, I get these errors:
(note: the first 3 warnings about mpi_paffinity_alone do not always
come up, so I am not sure if it is the core of the problem.)

dongting@mist ~/project1/mpi4py-1.2.1 $ mpirun -np 3 python demo/
helloworld.py
--------------------------------------------------------------------------
The MCA parameter "mpi_paffinity_alone" was set to a nonzero value,
but Open MPI was unable to bind MPI_COMM_WORLD rank 0 to a processor.

Typical causes for this problem include:

- A node was oversubscribed (more processes than processors), in
which case Open MPI will not bind any processes on that node
- A startup mechanism was used which did not tell Open MPI which
processors to bind processes to
--------------------------------------------------------------------------
--------------------------------------------------------------------------
The MCA parameter "mpi_paffinity_alone" was set to a nonzero value,
but Open MPI was unable to bind MPI_COMM_WORLD rank 1 to a processor.

Typical causes for this problem include:

- A node was oversubscribed (more processes than processors), in
which case Open MPI will not bind any processes on that node
- A startup mechanism was used which did not tell Open MPI which
processors to bind processes to
--------------------------------------------------------------------------
--------------------------------------------------------------------------
The MCA parameter "mpi_paffinity_alone" was set to a nonzero value,
but Open MPI was unable to bind MPI_COMM_WORLD rank 2 to a processor.

Typical causes for this problem include:

- A node was oversubscribed (more processes than processors), in
which case Open MPI will not bind any processes on that node
- A startup mechanism was used which did not tell Open MPI which
processors to bind processes to
--------------------------------------------------------------------------
[mist:16356] *** Process received signal ***
[mist:16356] Signal: Segmentation fault (11)
[mist:16356] Signal code: Address not mapped (1)
[mist:16356] Failing at address: (nil)
[mist:16356] [ 0] /lib64/libpthread.so.0 [0x3195e0de70]
[mist:16356] [ 1] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_btl_sm.so(mca_btl_sm_component_progress+0x1ad)
[0x2b6bc950a70d]
[mist:16356] [ 2] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_bml_r2.so(mca_bml_r2_progress+0x2a) [0x2b6bc90ff05a]
[mist:16356] [ 3] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libopen-pal.so.0(opal_progress+0x55) [0x2b6bc41178a5]
[mist:16356] [ 4] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_oob_tcp.so(mca_oob_tcp_msg_wait+0x1a) [0x2b6bc520229a]
[mist:16356] [ 5] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_oob_tcp.so(mca_oob_tcp_recv+0x42b) [0x2b6bc52067bb]
[mist:16356] [ 6] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libopen-rte.so.0(mca_oob_recv_packed+0x33) [0x2b6bc3edcb33]
[mist:16356] [ 7] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_gpr_proxy.so(orte_gpr_proxy_put+0x219) [0x2b6bc5616c79]
[mist:16356] [ 8] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libopen-rte.so.0(orte_smr_base_set_proc_state+0x2f4) [0x2b6bc3ef3654]
[mist:16356] [ 9] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libmpi.so.0(ompi_mpi_init+0x820) [0x2b6bc3c49950]
[mist:16356] [10] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libmpi.so.0(PMPI_Init_thread+0x120) [0x2b6bc3c6e2f0]
[mist:16356] [11] /mnt/netapp/home1/dongting/lib64/python/mpi4py/
MPI.so(initMPI+0x208c0) [0x2b6bc39c6ab0]
[mist:16356] [12] /usr/lib64/libpython2.4.so.
1.0(_PyImport_LoadDynamicModule+0xbd) [0x31a10acfad]
[mist:16356] [13] /usr/lib64/libpython2.4.so.1.0 [0x31a10ab4dd]
[mist:16356] [14] /usr/lib64/libpython2.4.so.1.0 [0x31a10ab772]
[mist:16356] [15] /usr/lib64/libpython2.4.so.
1.0(PyImport_ImportModuleEx+0x279) [0x31a10abd49]
[mist:16356] [16] /usr/lib64/libpython2.4.so.1.0 [0x31a108c5d3]
[mist:16356] [17] /usr/lib64/libpython2.4.so.1.0(PyObject_Call+0x10)
[0x31a1035fb0]
[mist:16356] [18] /usr/lib64/libpython2.4.so.
1.0(PyEval_CallObjectWithKeywords+0x6d) [0x31a108f55d]
[mist:16357] *** Process received signal ***
[mist:16357] Signal: Segmentation fault (11)
[mist:16357] Signal code: Address not mapped (1)
[mist:16357] Failing at address: (nil)
[mist:16358] *** Process received signal ***
[mist:16358] Signal: Segmentation fault (11)
[mist:16358] Signal code: Address not mapped (1)
[mist:16358] Failing at address: (nil)
[mist:16358] [ 0] /lib64/libpthread.so.0 [0x3195e0de70]
[mist:16358] [ 1] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_btl_sm.so(mca_btl_sm_component_progress+0x1ad)
[0x2b755e4cb70d]
[mist:16358] [ 2] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_bml_r2.so(mca_bml_r2_progress+0x2a) [0x2b755e0c005a]
[mist:16358] [ 3] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libopen-pal.so.0(opal_progress+0x55) [0x2b75590d88a5]
[mist:16358] [ 4] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_oob_tcp.so(mca_oob_tcp_msg_wait+0x1a) [0x2b755a1c329a]
[mist:16358] [ 5] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_oob_tcp.so(mca_oob_tcp_recv+0x42b) [0x2b755a1c77bb]
[mist:16358] [ 6] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libopen-rte.so.0(mca_oob_recv_packed+0x33) [0x2b7558e9db33]
[mist:16358] [ 7] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libopen-rte.so.0(mca_oob_xcast+0xb06) [0x2b7558e9e946]
[mist:16358] [ 8] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libmpi.so.0(ompi_mpi_init+0x855) [0x2b7558c0a985]
[mist:16358] [ 9] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libmpi.so.0(PMPI_Init_thread+0x120) [0x2b7558c2f2f0]
[mist:16358] [10] /mnt/netapp/home1/dongting/lib64/python/mpi4py/
MPI.so(initMPI+0x208c0) [0x2b7558987ab0]
[mist:16358] [11] /usr/lib64/libpython2.4.so.
1.0(_PyImport_LoadDynamicModule+0xbd) [0x31a10acfad]
[mist:16358] [12] /usr/lib64/libpython2.4.so.1.0 [0x31a10ab4dd]
[mist:16358] [13] /usr/lib64/libpython2.4.so.1.0 [0x31a10ab772]
[mist:16358] [14] /usr/lib64/libpython2.4.so.
1.0(PyImport_ImportModuleEx+0x279) [0x31a10abd49]
[mist:16358] [15] /usr/lib64/libpython2.4.so.1.0 [0x31a108c5d3]
[mist:16358] [16] /usr/lib64/libpython2.4.so.1.0(PyObject_Call+0x10)
[0x31a1035fb0]
[mist:16358] [17] /usr/lib64/libpython2.4.so.
1.0(PyEval_CallObjectWithKeywords+0x6d) [0x31a108f55d]
[mist:16358] [18] /usr/lib64/libpython2.4.so.1.0(PyEval_EvalFrame
+0x125a) [0x31a109123a]
[mist:16358] [19] /usr/lib64/libpython2.4.so.1.0(PyEval_EvalCodeEx
+0x925) [0x31a1095905]
[mist:16358] [20] /usr/lib64/libpython2.4.so.1.0(PyEval_EvalCode+0x32)
[0x31a1095952]
[mist:16358] [21] /usr/lib64/libpython2.4.so.1.0 [0x31a10b1fa9]
[mist:16358] [22] /usr/lib64/libpython2.4.so.
1.0(PyRun_SimpleFileExFlags+0x1a8) [0x31a10b3458]
[mist:16358] [23] /usr/lib64/libpython2.4.so.1.0(Py_Main+0xa5d)
[0x31a10b989d]
[mist:16358] [24] /lib64/libc.so.6(__libc_start_main+0xf4)
[0x319521d8b4]
[mist:16358] [25] python [0x400629]
[mist:16358] *** End of error message ***
[mist:16356] [19] /usr/lib64/libpython2.4.so.1.0(PyEval_EvalFrame
+0x125a) [0x31a109123a]
[mist:16356] [20] /usr/lib64/libpython2.4.so.1.0(PyEval_EvalCodeEx
+0x925) [0x31a1095905]
[mist:16356] [21] /usr/lib64/libpython2.4.so.1.0(PyEval_EvalCode+0x32)
[0x31a1095952]
[mist:16356] [22] /usr/lib64/libpython2.4.so.1.0 [0x31a10b1fa9]
[mist:16356] [23] /usr/lib64/libpython2.4.so.
1.0(PyRun_SimpleFileExFlags+0x1a8) [0x31a10b3458]
[mist:16356] [24] /usr/lib64/libpython2.4.so.1.0(Py_Main+0xa5d)
[0x31a10b989d]
[mist:16356] [25] /lib64/libc.so.6(__libc_start_main+0xf4)
[0x319521d8b4]
[mist:16356] [26] python [0x400629]
[mist:16356] *** End of error message ***
[mist:16357] [ 0] /lib64/libpthread.so.0 [0x3195e0de70]
[mist:16357] [ 1] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_btl_sm.so(mca_btl_sm_component_progress+0x1ad)
[0x2b45e26db70d]
[mist:16357] [ 2] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_bml_r2.so(mca_bml_r2_progress+0x2a) [0x2b45e22d005a]
[mist:16357] [ 3] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libopen-pal.so.0(opal_progress+0x55) [0x2b45dd2e88a5]
[mist:16357] [ 4] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_oob_tcp.so(mca_oob_tcp_msg_wait+0x1a) [0x2b45de3d329a]
[mist:16357] [ 5] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_oob_tcp.so(mca_oob_tcp_recv+0x42b) [0x2b45de3d77bb]
[mist:16357] [ 6] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libopen-rte.so.0(mca_oob_recv_packed+0x33) [0x2b45dd0adb33]
[mist:16357] [ 7] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_gpr_proxy.so(orte_gpr_proxy_put+0x219) [0x2b45de7e7c79]
[mist:16357] [ 8] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libopen-rte.so.0(orte_smr_base_set_proc_state+0x2f4) [0x2b45dd0c4654]
[mist:16357] [ 9] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libmpi.so.0(ompi_mpi_init+0x820) [0x2b45dce1a950]
[mist:16357] [10] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libmpi.so.0(PMPI_Init_thread+0x120) [0x2b45dce3f2f0]
[mist:16357] [11] /mnt/netapp/home1/dongting/lib64/python/mpi4py/
MPI.so(initMPI+0x208c0) [0x2b45dcb97ab0]
[mist:16357] [12] /usr/lib64/libpython2.4.so.
1.0(_PyImport_LoadDynamicModule+0xbd) [0x31a10acfad]
[mist:16357] [13] /usr/lib64/libpython2.4.so.1.0 [0x31a10ab4dd]
[mist:16357] [14] /usr/lib64/libpython2.4.so.1.0 [0x31a10ab772]
[mist:16357] [15] /usr/lib64/libpython2.4.so.
1.0(PyImport_ImportModuleEx+0x279) [0x31a10abd49]
[mist:16357] [16] /usr/lib64/libpython2.4.so.1.0 [0x31a108c5d3]
[mist:16357] [17] /usr/lib64/libpython2.4.so.1.0(PyObject_Call+0x10)
[0x31a1035fb0]
[mist:16357] [18] /usr/lib64/libpython2.4.so.
1.0(PyEval_CallObjectWithKeywords+0x6d) [0x31a108f55d]
[mist:16357] [19] /usr/lib64/libpython2.4.so.1.0(PyEval_EvalFrame
+0x125a) [0x31a109123a]
[mist:16357] [20] /usr/lib64/libpython2.4.so.1.0(PyEval_EvalCodeEx
+0x925) [0x31a1095905]
[mist:16357] [21] /usr/lib64/libpython2.4.so.1.0(PyEval_EvalCode+0x32)
[0x31a1095952]
[mist:16357] [22] /usr/lib64/libpython2.4.so.1.0 [0x31a10b1fa9]
[mist:16357] [23] /usr/lib64/libpython2.4.so.
1.0(PyRun_SimpleFileExFlags+0x1a8) [0x31a10b3458]
[mist:16357] [24] /usr/lib64/libpython2.4.so.1.0(Py_Main+0xa5d)
[0x31a10b989d]
[mist:16357] [25] /lib64/libc.so.6(__libc_start_main+0xf4)
[0x319521d8b4]
[mist:16357] [26] python [0x400629]
[mist:16357] *** End of error message ***


Any idea what is going on?

Thanks,
Dongting

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[Lisandro Dalcin]

First of all, you are using a very outdated Open MPI, however I
understand that that is likely out of your control.

The traceback you sent seems to fail deep inside MPI_Init_thread, and
in turn inside /lib64/libpthread.so.0 . It is known that older Open
MPI versions had issues with thread support.

Could you try a few things in order to figure out if this is an issue
with thread support?

1) Try to compile (with mpicc) and run(with mpiexec) the C program
demo/helloworld.c

2) Add the two lines below at the VERY beginning of helloworld.py and
next try to mpiexec it again:

import mpi4py.rc
mpi4py.rc.threaded = False



--
Lisandro Dalcin
---------------
CIMEC (INTEC/CONICET-UNL)
Predio CONICET-Santa Fe
Colectora RN 168 Km 472, Paraje El Pozo
Tel: +54-342-4511594 (ext 1011)
Tel/Fax: +54-342-4511169

[Dongting]

On May 14, 7:14 am, Lisandro Dalcin <dalc...@gmail.com> wrote:
>
> First of all, you are using a very outdated Open MPI, however I
> understand that that is likely out of your control.
>

Thanks for pointing that out. I did not realize that I have been using
an outdated version of Open MPI.
There are many versions available on this cluster that I am using, and
after I changed to a version 1.4.1 everything seems to work fine now.


Dongting

[Lisandro Dalcin]

On 14 May 2010 16:04, Dongting <begi...@gmail.com> wrote:
>
>
> On May 14, 7:14 am, Lisandro Dalcin <dalc...@gmail.com> wrote:
>>
>> First of all, you are using a very outdated Open MPI, however I
>> understand that that is likely out of your control.
>>
>
> Thanks for pointing that out. I did not realize that I have been using
> an outdated version of Open MPI.
> There are many versions available on this cluster that I am using, and
> after I changed to a version 1.4.1 everything seems to work fine now.
>

Any chance you could still try my previous suggestions with 1.2.1? I
try to maintain mpi4py working with any MPI out there, as other users
are not as lucky as you and they do not have the choice of switching
to updated MPI's. If you do not have the time, then never mind; thanks
anyway.

--
Lisandro Dalcin
---------------
CIMEC (INTEC/CONICET-UNL)
Predio CONICET-Santa Fe
Colectora RN 168 Km 472, Paraje El Pozo
Tel: +54-342-4511594 (ext 1011)
Tel/Fax: +54-342-4511169

[Dongting]

For sure. Glad to be able to help :)

On May 14, 7:14 am, Lisandro Dalcin <dalc...@gmail.com> wrote:

> Could you try a few things in order to figure out if this is an issue
> with thread support?
>
> 1) Try to compile (with mpicc) and run(with mpiexec) the C program
> demo/helloworld.c
>

This produced a lot of errors:

dongting@mist ~/project1/mpi4py-1.2.1/demo $ mpiexec -n 3
helloworld.out

[mist:03254] *** Process received signal ***
[mist:03253] *** Process received signal ***
[mist:03253] Signal: Segmentation fault (11)
[mist:03253] Signal code: Address not mapped (1)
[mist:03253] Failing at address: (nil)
[mist:03254] Signal: Segmentation fault (11)
[mist:03254] Signal code: Address not mapped (1)
[mist:03254] Failing at address: (nil)
[mist:03253] [ 0] /lib64/libpthread.so.0 [0x3195e0de70]
[mist:03253] [ 1] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_btl_sm.so(mca_btl_sm_component_progress+0x1ad)
[0x2b04b415470d]
[mist:03253] [ 2] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_bml_r2.so(mca_bml_r2_progress+0x2a) [0x2b04b3d4905a]
[mist:03253] [ 3] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libopen-pal.so.0(opal_progress+0x55) [0x2b04aed818a5]
[mist:03253] [ 4] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_oob_tcp.so(mca_oob_tcp_msg_wait+0x1a) [0x2b04afe4c29a]
[mist:03253] [ 5] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_oob_tcp.so(mca_oob_tcp_recv+0x42b) [0x2b04afe507bb]
[mist:03253] [ 6] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libopen-rte.so.0(mca_oob_recv_packed+0x33) [0x2b04aeb46b33]
[mist:03253] [ 7] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_gpr_proxy.so(orte_gpr_proxy_put+0x219) [0x2b04b0260c79]
[mist:03253] [ 8] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libopen-rte.so.0(orte_smr_base_set_proc_state+0x2f4) [0x2b04aeb5d654]
[mist:03253] [ 9] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libmpi.so.0(ompi_mpi_init+0x820) [0x2b04ae8b3950]
[mist:03253] [10] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libmpi.so.0(PMPI_Init_thread+0x60) [0x2b04ae8d8230]
[mist:03253] [11] helloworld.out(main+0x37) [0x40090f]
[mist:03253] [12] /lib64/libc.so.6(__libc_start_main+0xf4)
[0x319521d8b4]
[mist:03253] [13] helloworld.out [0x400829]
[mist:03253] *** End of error message ***
[mist:03255] *** Process received signal ***
[mist:03255] Signal: Segmentation fault (11)
[mist:03255] Signal code: Address not mapped (1)
[mist:03255] Failing at address: (nil)
[mist:03255] [ 0] /lib64/libpthread.so.0 [0x3195e0de70]
[mist:03255] [ 1] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_btl_sm.so(mca_btl_sm_component_progress+0x1ad)
[0x2ba95c2b870d]
[mist:03255] [ 2] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_bml_r2.so(mca_bml_r2_progress+0x2a) [0x2ba95bead05a]
[mist:03255] [ 3] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libopen-pal.so.0(opal_progress+0x55) [0x2ba956ee58a5]
[mist:03255] [ 4] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_oob_tcp.so(mca_oob_tcp_msg_wait+0x1a) [0x2ba957fb029a]
[mist:03255] [ 5] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_oob_tcp.so(mca_oob_tcp_recv+0x42b) [0x2ba957fb47bb]
[mist:03255] [ 6] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libopen-rte.so.0(mca_oob_recv_packed+0x33) [0x2ba956caab33]
[mist:03255] [ 7] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libopen-rte.so.0(mca_oob_xcast+0xb06) [0x2ba956cab946]
[mist:03255] [ 8] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libmpi.so.0(ompi_mpi_init+0x855) [0x2ba956a17985]
[mist:03255] [ 9] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libmpi.so.0(PMPI_Init_thread+0x60) [0x2ba956a3c230]
[mist:03255] [10] helloworld.out(main+0x37) [0x40090f]
[mist:03255] [11] /lib64/libc.so.6(__libc_start_main+0xf4)
[0x319521d8b4]
[mist:03255] [12] helloworld.out [0x400829]
[mist:03255] *** End of error message ***
[mist:03254] [ 0] /lib64/libpthread.so.0 [0x3195e0de70]
[mist:03254] [ 1] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_btl_sm.so(mca_btl_sm_component_progress+0x1ad)
[0x2b32f834270d]
[mist:03254] [ 2] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_bml_r2.so(mca_bml_r2_progress+0x2a) [0x2b32f7f3705a]
[mist:03254] [ 3] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libopen-pal.so.0(opal_progress+0x55) [0x2b32f2f6f8a5]
[mist:03254] [ 4] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_oob_tcp.so(mca_oob_tcp_msg_wait+0x1a) [0x2b32f403a29a]
[mist:03254] [ 5] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_oob_tcp.so(mca_oob_tcp_recv+0x42b) [0x2b32f403e7bb]
[mist:03254] [ 6] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libopen-rte.so.0(mca_oob_recv_packed+0x33) [0x2b32f2d34b33]
[mist:03254] [ 7] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
openmpi/mca_gpr_proxy.so(orte_gpr_proxy_put+0x219) [0x2b32f444ec79]
[mist:03254] [ 8] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libopen-rte.so.0(orte_smr_base_set_proc_state+0x2f4) [0x2b32f2d4b654]
[mist:03254] [ 9] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libmpi.so.0(ompi_mpi_init+0x820) [0x2b32f2aa1950]
[mist:03254] [10] /usr/local/packages/openmpi-1.2.6/gnu-4.1.2-tm/lib/
libmpi.so.0(PMPI_Init_thread+0x60) [0x2b32f2ac6230]
[mist:03254] [11] helloworld.out(main+0x37) [0x40090f]
[mist:03254] [12] /lib64/libc.so.6(__libc_start_main+0xf4)
[0x319521d8b4]
[mist:03254] [13] helloworld.out [0x400829]
[mist:03254] *** End of error message ***

> 2) Add the two lines below at the VERY beginning of helloworld.py and
> next try to mpiexec it again:
>
> import mpi4py.rc
> mpi4py.rc.threaded = False
>

This worked:

dongting@mist ~/project1/mpi4py-1.2.1/demo $ mpiexec -n 3 python

helloworld.py
--------------------------------------------------------------------------
The MCA parameter "mpi_paffinity_alone" was set to a nonzero value,
but Open MPI was unable to bind MPI_COMM_WORLD rank 0 to a processor.

Typical causes for this problem include:

- A node was oversubscribed (more processes than processors), in
which case Open MPI will not bind any processes on that node
- A startup mechanism was used which did not tell Open MPI which
processors to bind processes to
--------------------------------------------------------------------------
--------------------------------------------------------------------------
The MCA parameter "mpi_paffinity_alone" was set to a nonzero value,

but Open MPI was unable to bind MPI_COMM_WORLD rank 2 to a processor.

Typical causes for this problem include:

- A node was oversubscribed (more processes than processors), in
which case Open MPI will not bind any processes on that node
- A startup mechanism was used which did not tell Open MPI which
processors to bind processes to
--------------------------------------------------------------------------

--------------------------------------------------------------------------
The MCA parameter "mpi_paffinity_alone" was set to a nonzero value,
but Open MPI was unable to bind MPI_COMM_WORLD rank 1 to a processor.

Typical causes for this problem include:

- A node was oversubscribed (more processes than processors), in
which case Open MPI will not bind any processes on that node
- A startup mechanism was used which did not tell Open MPI which
processors to bind processes to
--------------------------------------------------------------------------

Hello, World! I am process 2 of 3 on mist.<domainname>.
Hello, World! I am process 0 of 3 on mist.<domainname>.
Hello, World! I am process 1 of 3 on mist.<domainname>.

[Lisandro Dalcin]

On 15 May 2010 00:59, Dongting <begi...@gmail.com> wrote:
> For sure. Glad to be able to help :)
>
> On May 14, 7:14 am, Lisandro Dalcin <dalc...@gmail.com> wrote:
>> Could you try a few things in order to figure out if this is an issue
>> with thread support?
>>
>> 1) Try to compile (with mpicc) and run(with mpiexec) the C program
>> demo/helloworld.c
>>
>
> This produced a lot of errors:
>
> dongting@mist ~/project1/mpi4py-1.2.1/demo $ mpiexec -n 3
> helloworld.out
>

>> 2) Add the two lines below at the VERY beginning of helloworld.py and
>> next try to mpiexec it again:
>>
>> import mpi4py.rc
>> mpi4py.rc.threaded = False
>>
>
> This worked:
>
> dongting@mist ~/project1/mpi4py-1.2.1/demo $ mpiexec -n 3 python
> helloworld.py

This more or less confirms that the issue is related to initializing
MPI with MPI_Init_thread().

Many thanks,

--
Lisandro Dalcin
---------------
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