Re: [OMPI users] Problem with compilation : statically linked applications
__cxa_get_exception_ptr should be defined in libstdc++ shared library. --Nysal On Mon, Jun 14, 2010 at 5:51 AM, HeeJin Kim wrote: > Dear all, > > I had built openmpi-1.4.2 with: > configure CC=icc CXX=icpc F77=ifort FC=ifort > --prefix=/home/biduri/program/openmpi --enable-mpi-threads --enable-static > > And I have a problem during compilation of q-chem software which uses > openmpi. > > > /home/biduri/program/openmpi/lib/libopen-pal.a(dlopen.o): In function > `vm_open': > loaders/dlopen.c:(.text+0xad): warning: Using 'dlopen' in statically linked > applications requires at runtime the shared libraries from the glibc version > used for linking > /home/biduri/qchem/par_qchem_op/ccman/ccman.a(properties.o): In function > `CalcNonRelaxedTransDipole(Spin, int, int, Spin, int, int, OPDM&, OPDM&, > double, int, signed char, _IO_FILE*, signed char, signed char)': > properties.C:(.text+0x3df8): undefined reference to > `__cxa_get_exception_ptr' > /home/biduri/qchem/par_qchem_op/ccman/ccman.a(properties.o): In function > `CalcSOCs(AlphaBetaMatr&, BlockTensor&, KMatrix&)': > properties.C:(.text+0x52fc): undefined reference to > `__cxa_get_exception_ptr' > /home/biduri/qchem/par_qchem_op/ccman/ccman.a(ccsd_calc.o): In function > `CCSD_Calc::CalculateT(BlockTensor&, BlockTensor&, MutableBlockTensor&, > MutableBlockTensor&, signed char)': > ccsd_calc.C:(.text+0x2957): undefined reference to > `__cxa_get_exception_ptr' > /home/biduri/qchem/par_qchem_op/ccman/ccman.a(ccsd_calc.o): In function > `CCSD_Calc::CalcLambdaIntermed()': > ccsd_calc.C:(.text+0x4409): undefined reference to > `__cxa_get_exception_ptr' > > > Best, > Heejin > > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users >
Re: [OMPI users] ompi-restart failed
Hi all, I finally figured out the answer. I just put the parameter "-machinefile host" in the "ompi-restart" command and it restarted correctly. So is it unable to restart multi-threaded application on 1 node in OpenMPI? Nguyen Toan On Tue, Jun 8, 2010 at 12:07 AM, Nguyen Toan wrote: > Sorry, I just want to add 2 more things: > + I tried configure with and without --enable-ft-thread but nothing changed > + I also applied this patch for OpenMPI here and reinstalled but I got the > same error > > https://svn.open-mpi.org/trac/ompi/raw-attachment/ticket/2139/v1.4-preload-part1.diff > > Somebody helps? Thank you very much. > > Nguyen Toan > > > On Mon, Jun 7, 2010 at 11:51 PM, Nguyen Toan wrote: > >> Hello everyone, >> >> I'm using OpenMPI 1.4.2 with BLCR 0.8.2 to test checkpointing on 2 nodes >> but it failed to restart (Segmentation fault). >> Here are the details concerning my problem: >> >> + OS: Centos 5.4 >> + OpenMPI configure: >> ./configure --with-ft=cr --enable-ft-thread --enable-mpi-threads \ >> --with-blcr=/home/nguyen/opt/blcr >> --with-blcr-libdir=/home/nguyen/opt/blcr/lib \ >> --prefix=/home/nguyen/opt/openmpi \ >> --enable-mpirun-prefix-by-default >> + mpirun -am ft-enable-cr -machinefile host ./test >> >> I checkpointed the test program using "ompi-checkpoint -v -s PID" and the >> checkpoint file was created successfully. However it failed to restart using >> ompi-restart: >> *"mpirun noticed that process rank 0 with PID 21242 on node rc014.local >> exited on signal 11 (Segmentation fault)" >> * >> Did I miss something in the installation of OpenMPI? >> >> Regards, >> Nguyen Toan >> > >
[OMPI users] How to checkpoint atomic function in OpenMPI
Hi all,
I have a MPI program as follows:
---
int main(){
MPI_Init();
..
for (i=0; i<1; i++) {
my_atomic_func();
}
...
MPI_Finalize();
return 0;
}
The runtime of this program mainly involves in running the loop and
my_atomic_func() takes a little bit long.
Here I want my_atomic_func() to be operated atomically, but the timing of
checkpointing (by running ompi-checkpoint command) may be in the middle of
my_atomic_func() operation and hence ompi-restart may fail to restart
correctly.
So my question is:
+ At the checkpoint time (executing ompi-checkpoint), is there a way to let
OpenMPI wait until my_atomic_func() finishes its operation?
+ How does ompi-checkpoint operate to checkpoint MPI threads?
Regards,
Nguyen Toan
Re: [OMPI users] A problem with 'mpiexec -launch-agent'
Hi,
Am 13.06.2010 um 09:02 schrieb Zhang Linbo:
Hi,
I'm new to OpenMPI and have encountered a problem with mpiexec.
Since I need to set up the execution environment for OpenMPI programs
on the execution nodes, I use the following command line to launch an
OMPI program:
mpiexec -launch-agent /some_path/myscript
The problem is: the above command works fine if I invoke 'mpiexec'
without an absolute path just like above (assuming the PATH variable
is properly set), but if I prepend an absolute path to 'mpiexec',
e.g.:
/OMPI_dir/bin/mpiexec -launch-agent /some_path/myscript
using an absolute path is equivalent to use the --prefix option to
`mpiexec`. Both ways lead obviously to the erroneous behavior you
encounter.
then I get the following error message:
bash: -c: line 0: syntax error near unexpected token `('
bash: -c: line 0: ` PATH=/OMPI_dir/bin:$PATH ; export PATH ;
LD_LIBRARY_PATH=/OMPI_dir/lib:$LD_LIBRARY_PATH ; export
LD_LIBRARY_PATH ; /some_path/myscript /OMPI_dir/bin/(null) --
daemonize -mca ess env -mca orte_ess_jobid 1978662912 -mca
orte_ess_vpid 1 -mca orte_ess_num_procs 2 --hnp-uri
"1978662912.0;tcp://180.0.14.12:54844;tcp://190.0.14.12:54844"'
Reason seems to be, that in case of a given prefix the assembly of the
necessary command line includes some elements too much. I tried to
circumvent this by a new case in "orte/mca/plm/rsh/plm_rsh_module.c":
if (orted_prefix != NULL) {
asprintf (&final_cmd,
"%s%s%s PATH=%s/%s:$PATH ; export PATH ; "
"LD_LIBRARY_PATH=%s/%s:$LD_LIBRARY_PATH ;
export LD_LIBRARY_PATH ; "
"%s",
(opal_prefix != NULL ? "OPAL_PREFIX=" : ""),
(opal_prefix != NULL ? opal_prefix : ""),
(opal_prefix != NULL ? " ; export
OPAL_PREFIX;" : ""),
prefix_dir, bin_base,
prefix_dir, lib_base,
orted_prefix );
}
else {
asprintf (&final_cmd,
"%s%s%s PATH=%s/%s:$PATH ; export PATH ; "
"LD_LIBRARY_PATH=%s/%s:$LD_LIBRARY_PATH ;
export LD_LIBRARY_PATH ; "
"%s %s/%s/%s",
(opal_prefix != NULL ? "OPAL_PREFIX=" : ""),
(opal_prefix != NULL ? opal_prefix : ""),
(opal_prefix != NULL ? " ; export
OPAL_PREFIX;" : ""),
prefix_dir, bin_base,
prefix_dir, lib_base,
(orted_prefix != NULL ? orted_prefix : ""),
prefix_dir, bin_base,
orted_cmd);
}
The name of the agent is for sake of easiness stored in "opal_prefix"
AFAICS.
This is of course not a clean solution (as "opal_prefix" can't be used
any more), but more a proof of concept, as only sh-like shelle are
handled. Sure there are better ways to solve it. Anyway, it's a bug
and should be filed
-- Reuti
I'd like to know what causes the above problem and how should I deal
with it.
I want to use absolute pathname of mpiexec to avoid possible
inteferences
with other MPI installations. Thanks in advance.
LB
___
users mailing list
us...@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users
Re: [OMPI users] A problem with 'mpiexec -launch-agent'
Jeff and I are taking a look at the logic in that code now - I know we thought
we understood it back when we wrote it, but somehow it just doesn't look right
any more...
On Jun 14, 2010, at 4:13 PM, Reuti wrote:
> Hi,
>
> Am 13.06.2010 um 09:02 schrieb Zhang Linbo:
>
>> Hi,
>>
>> I'm new to OpenMPI and have encountered a problem with mpiexec.
>>
>> Since I need to set up the execution environment for OpenMPI programs
>> on the execution nodes, I use the following command line to launch an
>> OMPI program:
>>
>> mpiexec -launch-agent /some_path/myscript
>>
>> The problem is: the above command works fine if I invoke 'mpiexec'
>> without an absolute path just like above (assuming the PATH variable
>> is properly set), but if I prepend an absolute path to 'mpiexec', e.g.:
>>
>> /OMPI_dir/bin/mpiexec -launch-agent /some_path/myscript
>
> using an absolute path is equivalent to use the --prefix option to `mpiexec`.
> Both ways lead obviously to the erroneous behavior you encounter.
>
>
>> then I get the following error message:
>>
>> bash: -c: line 0: syntax error near unexpected token `('
>> bash: -c: line 0: ` PATH=/OMPI_dir/bin:$PATH ; export PATH ;
>> LD_LIBRARY_PATH=/OMPI_dir/lib:$LD_LIBRARY_PATH ; export LD_LIBRARY_PATH ;
>> /some_path/myscript /OMPI_dir/bin/(null) --daemonize -mca ess env -mca
>> orte_ess_jobid 1978662912 -mca orte_ess_vpid 1 -mca orte_ess_num_procs 2
>> --hnp-uri "1978662912.0;tcp://180.0.14.12:54844;tcp://190.0.14.12:54844"'
>
> Reason seems to be, that in case of a given prefix the assembly of the
> necessary command line includes some elements too much. I tried to circumvent
> this by a new case in "orte/mca/plm/rsh/plm_rsh_module.c":
>
>if (orted_prefix != NULL) {
>asprintf (&final_cmd,
> "%s%s%s PATH=%s/%s:$PATH ; export PATH ; "
> "LD_LIBRARY_PATH=%s/%s:$LD_LIBRARY_PATH ; export
> LD_LIBRARY_PATH ; "
> "%s",
> (opal_prefix != NULL ? "OPAL_PREFIX=" : ""),
> (opal_prefix != NULL ? opal_prefix : ""),
> (opal_prefix != NULL ? " ; export OPAL_PREFIX;" : ""),
> prefix_dir, bin_base,
> prefix_dir, lib_base,
> orted_prefix );
>}
>else {
>asprintf (&final_cmd,
> "%s%s%s PATH=%s/%s:$PATH ; export PATH ; "
> "LD_LIBRARY_PATH=%s/%s:$LD_LIBRARY_PATH ; export
> LD_LIBRARY_PATH ; "
> "%s %s/%s/%s",
> (opal_prefix != NULL ? "OPAL_PREFIX=" : ""),
> (opal_prefix != NULL ? opal_prefix : ""),
> (opal_prefix != NULL ? " ; export OPAL_PREFIX;" : ""),
> prefix_dir, bin_base,
> prefix_dir, lib_base,
> (orted_prefix != NULL ? orted_prefix : ""),
> prefix_dir, bin_base,
> orted_cmd);
>}
>
> The name of the agent is for sake of easiness stored in "opal_prefix" AFAICS.
>
> This is of course not a clean solution (as "opal_prefix" can't be used any
> more), but more a proof of concept, as only sh-like shelle are handled. Sure
> there are better ways to solve it. Anyway, it's a bug and should be filed
>
> -- Reuti
>
>
>> I'd like to know what causes the above problem and how should I deal with it.
>> I want to use absolute pathname of mpiexec to avoid possible inteferences
>> with other MPI installations. Thanks in advance.
>>
>> LB
>>
>>
>> ___
>> 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] A problem with 'mpiexec -launch-agent'
Am 15.06.2010 um 00:26 schrieb Ralph Castain:
Jeff and I are taking a look at the logic in that code now - I know
we thought we understood it back when we wrote it, but somehow it
just doesn't look right any more...
To avoid confusion: I meant "orted_prefix" below which holds the name
of the launch-agent and can't be used with this demonstration fix.
Sorry for the typo.
-- Reuti
On Jun 14, 2010, at 4:13 PM, Reuti wrote:
Hi,
Am 13.06.2010 um 09:02 schrieb Zhang Linbo:
Hi,
I'm new to OpenMPI and have encountered a problem with mpiexec.
Since I need to set up the execution environment for OpenMPI
programs
on the execution nodes, I use the following command line to launch
an
OMPI program:
mpiexec -launch-agent /some_path/myscript
The problem is: the above command works fine if I invoke 'mpiexec'
without an absolute path just like above (assuming the PATH variable
is properly set), but if I prepend an absolute path to 'mpiexec',
e.g.:
/OMPI_dir/bin/mpiexec -launch-agent /some_path/myscript
using an absolute path is equivalent to use the --prefix option to
`mpiexec`. Both ways lead obviously to the erroneous behavior you
encounter.
then I get the following error message:
bash: -c: line 0: syntax error near unexpected token `('
bash: -c: line 0: ` PATH=/OMPI_dir/bin:$PATH ; export PATH ;
LD_LIBRARY_PATH=/OMPI_dir/lib:$LD_LIBRARY_PATH ; export
LD_LIBRARY_PATH ; /some_path/myscript /OMPI_dir/bin/(null) --
daemonize -mca ess env -mca orte_ess_jobid 1978662912 -mca
orte_ess_vpid 1 -mca orte_ess_num_procs 2 --hnp-uri
"1978662912.0;tcp://180.0.14.12:54844;tcp://190.0.14.12:54844"'
Reason seems to be, that in case of a given prefix the assembly of
the necessary command line includes some elements too much. I tried
to circumvent this by a new case in "orte/mca/plm/rsh/
plm_rsh_module.c":
if (orted_prefix != NULL) {
asprintf (&final_cmd,
"%s%s%s PATH=%s/%s:$PATH ; export PATH ; "
"LD_LIBRARY_PATH=%s/%s:$LD_LIBRARY_PATH ;
export LD_LIBRARY_PATH ; "
"%s",
(opal_prefix != NULL ? "OPAL_PREFIX=" : ""),
(opal_prefix != NULL ? opal_prefix : ""),
(opal_prefix != NULL ? " ; export
OPAL_PREFIX;" : ""),
prefix_dir, bin_base,
prefix_dir, lib_base,
orted_prefix );
}
else {
asprintf (&final_cmd,
"%s%s%s PATH=%s/%s:$PATH ; export PATH ; "
"LD_LIBRARY_PATH=%s/%s:$LD_LIBRARY_PATH ;
export LD_LIBRARY_PATH ; "
"%s %s/%s/%s",
(opal_prefix != NULL ? "OPAL_PREFIX=" : ""),
(opal_prefix != NULL ? opal_prefix : ""),
(opal_prefix != NULL ? " ; export
OPAL_PREFIX;" : ""),
prefix_dir, bin_base,
prefix_dir, lib_base,
(orted_prefix != NULL ? orted_prefix : ""),
prefix_dir, bin_base,
orted_cmd);
}
The name of the agent is for sake of easiness stored in
"opal_prefix" AFAICS.
This is of course not a clean solution (as "opal_prefix" can't be
used any more), but more a proof of concept, as only sh-like shelle
are handled. Sure there are better ways to solve it. Anyway, it's a
bug and should be filed
-- Reuti
I'd like to know what causes the above problem and how should I
deal with it.
I want to use absolute pathname of mpiexec to avoid possible
inteferences
with other MPI installations. Thanks in advance.
LB
___
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] A problem with 'mpiexec -launch-agent'
On Tue, 2010-06-15 at 00:13 +0200, Reuti wrote: > Hi, > > Am 13.06.2010 um 09:02 schrieb Zhang Linbo: > > > Hi, > > > > I'm new to OpenMPI and have encountered a problem with mpiexec. > > > > Since I need to set up the execution environment for OpenMPI programs > > on the execution nodes, I use the following command line to launch an > > OMPI program: > > > > mpiexec -launch-agent /some_path/myscript > > > > The problem is: the above command works fine if I invoke 'mpiexec' > > without an absolute path just like above (assuming the PATH variable > > is properly set), but if I prepend an absolute path to 'mpiexec', > > e.g.: > > > > /OMPI_dir/bin/mpiexec -launch-agent /some_path/myscript > > using an absolute path is equivalent to use the --prefix option to > `mpiexec`. Both ways lead obviously to the erroneous behavior you > encounter. Hi folks Speaking as no more than an uneducated user, having the behaviour change depending on invoking by an absolute path or invoking by some unspecified (potentially shell-dependent) path magic seems like a bad idea. As a long-time *nix user, this just rubs me the wrong way. Ciao Terry -- Dr. Terry Frankcombe Research School of Chemistry, Australian National University Ph: (+61) 0417 163 509Skype: terry.frankcombe
Re: [OMPI users] A problem with 'mpiexec -launch-agent'
It isn't our intention either - still looking at this to see what is going on. On Jun 14, 2010, at 6:24 PM, Terry Frankcombe wrote: > On Tue, 2010-06-15 at 00:13 +0200, Reuti wrote: >> Hi, >> >> Am 13.06.2010 um 09:02 schrieb Zhang Linbo: >> >>> Hi, >>> >>> I'm new to OpenMPI and have encountered a problem with mpiexec. >>> >>> Since I need to set up the execution environment for OpenMPI programs >>> on the execution nodes, I use the following command line to launch an >>> OMPI program: >>> >>> mpiexec -launch-agent /some_path/myscript >>> >>> The problem is: the above command works fine if I invoke 'mpiexec' >>> without an absolute path just like above (assuming the PATH variable >>> is properly set), but if I prepend an absolute path to 'mpiexec', >>> e.g.: >>> >>> /OMPI_dir/bin/mpiexec -launch-agent /some_path/myscript >> >> using an absolute path is equivalent to use the --prefix option to >> `mpiexec`. Both ways lead obviously to the erroneous behavior you >> encounter. > > Hi folks > > Speaking as no more than an uneducated user, having the behaviour change > depending on invoking by an absolute path or invoking by some > unspecified (potentially shell-dependent) path magic seems like a bad > idea. > > As a long-time *nix user, this just rubs me the wrong way. > > Ciao > Terry > > > -- > Dr. Terry Frankcombe > Research School of Chemistry, Australian National University > Ph: (+61) 0417 163 509Skype: terry.frankcombe > > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
