[mpich-discuss] cryptic (to me) error
Dave Goodell
goodell at mcs.anl.gov
Fri Sep 3 09:20:44 CDT 2010
Try setting HYDRA_HOST_FILE=your_machine_file_here
This will make hydra act as though you passed "-f your machine_file_here" to every mpiexec.
http://wiki.mcs.anl.gov/mpich2/index.php/Using_the_Hydra_Process_Manager#Environment_Settings
-Dave
On Sep 3, 2010, at 5:00 AM CDT, SULLIVAN David (AREVA) wrote:
> I was wondering about that. Is there a configuration file that sets up the cluster and defines which node to run on? Would that make the issue any clearer?
>
> Thanks,
>
> Dave
>
>
> -----Original Message-----
> From: mpich-discuss-bounces at mcs.anl.gov on behalf of Rajeev Thakur
> Sent: Thu 9/2/2010 10:22 PM
> To: mpich-discuss at mcs.anl.gov
> Subject: Re: [mpich-discuss] cryptic (to me) error
>
> There might be some connection issues between the two machines. The MPICH2 test suite that you ran with "make testing" probably ran on a single machine.
>
> On Sep 2, 2010, at 6:27 PM, SULLIVAN David (AREVA) wrote:
>
>> The error occurs immediately- I don't think it even starts the executable. It does work on the single machine with 4 processes.
>>
>>
>> -----Original Message-----
>> From: mpich-discuss-bounces at mcs.anl.gov on behalf of Rajeev Thakur
>> Sent: Thu 9/2/2010 4:34 PM
>> To: mpich-discuss at mcs.anl.gov
>> Subject: Re: [mpich-discuss] cryptic (to me) error
>>
>> Does it run with 2 processes on a single machine?
>>
>>
>> On Sep 2, 2010, at 2:38 PM, SULLIVAN David (AREVA) wrote:
>>
>>> That fixed the compile. Thanks!
>>>
>>> The latest release does not fix the issues I am having though. Cpi works
>>> fine, the test suit is certainly improved (see summary.xml output)
>>> though when I try to use mcnp it still crashes in the same way (see
>>> error.txt)
>>>
>>> -----Original Message-----
>>> From: mpich-discuss-bounces at mcs.anl.gov
>>> [mailto:mpich-discuss-bounces at mcs.anl.gov] On Behalf Of Anthony Chan
>>> Sent: Thursday, September 02, 2010 1:38 PM
>>> To: mpich-discuss at mcs.anl.gov
>>> Subject: Re: [mpich-discuss] cryptic (to me) error
>>>
>>>
>>> There is a bug in 1.3b1 about the option --enable-fc. Since Fortran 90
>>> is enabled by default, so remove the --enable-fc from your configure
>>> command and try again. If there is error again, send us the configure
>>> output as you seen on your screen (See README) instead of config.log.
>>>
>>> A.Chan
>>>
>>> ----- "SULLIVAN David (AREVA)" <David.Sullivan at areva.com> wrote:
>>>
>>>> Failure again.
>>>> The 1.3 beta version will not compile with Intel 10.1. It bombs at the
>>>
>>>> configuration script:
>>>>
>>>> checking for Fortran flag needed to allow free-form source... unknown
>>>> configure: WARNING: Fortran 90 test being disabled because the
>>>> /home/dfs/mpich2-1.3b1/bin/mpif90 compiler does not accept a .f90
>>>> extension
>>>> configure: error: Fortran does not accept free-form source
>>>> configure: error: ./configure failed for test/mpi
>>>>
>>>> I have attached to config.log
>>>>
>>>> -----Original Message-----
>>>> From: mpich-discuss-bounces at mcs.anl.gov
>>>> [mailto:mpich-discuss-bounces at mcs.anl.gov] On Behalf Of Rajeev Thakur
>>>> Sent: Thursday, September 02, 2010 12:11 PM
>>>> To: mpich-discuss at mcs.anl.gov
>>>> Subject: Re: [mpich-discuss] cryptic (to me) error
>>>>
>>>> Just try relinking with the new library at first.
>>>>
>>>> Rajeev
>>>>
>>>> On Sep 2, 2010, at 9:32 AM, SULLIVAN David (AREVA) wrote:
>>>>
>>>>> I saw that there was a newer beta. I was really hoping to find I
>>>> just
>>>>> configured something incorrectly. Will this not require me to
>>>> re-build
>>>>
>>>>> mcnp (the only program I run that uses mpi for parallel) if I change
>>>>
>>>>> the mpi version? If so, this is a bit of a hardship, requiring codes
>>>>
>>>>> to be revalidated. If not- I will try it in a second.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Dave
>>>>>
>>>>> -----Original Message-----
>>>>> From: mpich-discuss-bounces at mcs.anl.gov
>>>>> [mailto:mpich-discuss-bounces at mcs.anl.gov] On Behalf Of Dave
>>>> Goodell
>>>>> Sent: Thursday, September 02, 2010 10:27 AM
>>>>> To: mpich-discuss at mcs.anl.gov
>>>>> Subject: Re: [mpich-discuss] cryptic (to me) error
>>>>>
>>>>> Can you try the latest release (1.3b1) to see if that fixes the
>>>>> problems you are seeing with your application?
>>>>>
>>>>>
>>>> http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=
>>>>> do
>>>>> wnloads
>>>>>
>>>>> -Dave
>>>>>
>>>>> On Sep 2, 2010, at 9:15 AM CDT, SULLIVAN David (AREVA) wrote:
>>>>>
>>>>>> Another output file, hopefully of use.
>>>>>>
>>>>>> Thanks again
>>>>>>
>>>>>> Dave
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: mpich-discuss-bounces at mcs.anl.gov
>>>>>> [mailto:mpich-discuss-bounces at mcs.anl.gov] On Behalf Of SULLIVAN
>>>>>> David
>>>>>> (AREVA)
>>>>>> Sent: Thursday, September 02, 2010 8:20 AM
>>>>>> To: mpich-discuss at mcs.anl.gov
>>>>>> Subject: Re: [mpich-discuss] cryptic (to me) error
>>>>>>
>>>>>> First my apologies for the delay in continuing this thread.
>>>>>> Unfortunately I have not resolved it so if I can indulge the gurus
>>>>
>>>>>> and
>>>>>
>>>>>> developers once again...
>>>>>>
>>>>>> As suggested by Rajeev I ran the testing suit in the source
>>>> directory.
>>>>>> The output of errors, which are similar to what I was seeing when I
>>>>
>>>>>> ran
>>>>>> mcnp5 (v. 1.40 and 1.51), is attached.
>>>>>>
>>>>>> Any insights would be greatly appreciated,
>>>>>>
>>>>>> Dave
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: mpich-discuss-bounces at mcs.anl.gov
>>>>>> [mailto:mpich-discuss-bounces at mcs.anl.gov] On Behalf Of Rajeev
>>>> Thakur
>>>>>> Sent: Wednesday, August 04, 2010 3:06 PM
>>>>>> To: mpich-discuss at mcs.anl.gov
>>>>>> Subject: Re: [mpich-discuss] cryptic (to me) error
>>>>>>
>>>>>> Then one level above that directory (in the main MPICH2 source
>>>>>> directory), type make testing, which will run through the entire
>>>>>> MPICH2 test suite.
>>>>>>
>>>>>> Rajeev
>>>>>>
>>>>>> On Aug 4, 2010, at 2:04 PM, SULLIVAN David (AREVA) wrote:
>>>>>>
>>>>>>> Oh. That's embarrassing. Yea. I have those examples. It runs
>>>> with
>>>>>>> no
>>>>>>> problems:
>>>>>>>
>>>>>>> [dfs at aramis examples]$ mpiexec -host aramis -n 4 ./cpi Process 2
>>>> of
>>>>>>> 4
>>>>>
>>>>>>> is on aramis Process 3 of 4 is on aramis Process 0 of 4 is on
>>>> aramis
>>>>
>>>>>>> Process 1 of 4 is on aramis pi is approximately
>>>> 3.1415926544231239,
>>>>>>> Error is 0.0000000008333307 wall clock time = 0.000652
>>>>>>>
>>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: mpich-discuss-bounces at mcs.anl.gov
>>>>>>> [mailto:mpich-discuss-bounces at mcs.anl.gov] On Behalf Of Gus
>>>> Correa
>>>>>>> Sent: Wednesday, August 04, 2010 1:13 PM
>>>>>>> To: Mpich Discuss
>>>>>>> Subject: Re: [mpich-discuss] cryptic (to me) error
>>>>>>>
>>>>>>> Hi David
>>>>>>>
>>>>>>> I think the "examples" dir is not copied to the installation
>>>>>> directory.
>>>>>>> You may find it where you decompressed the MPICH2 tarball, in case
>>>>
>>>>>>> you
>>>>>>
>>>>>>> installed it from source.
>>>>>>> At least, this is what I have here.
>>>>>>>
>>>>>>> Gus Correa
>>>>>>>
>>>>>>>
>>>>>>> SULLIVAN David (AREVA) wrote:
>>>>>>>> Yea, that always bothered me. There is no such folder.
>>>>>>>> There are :
>>>>>>>> bin
>>>>>>>> etc
>>>>>>>> include
>>>>>>>> lib
>>>>>>>> sbin
>>>>>>>> share
>>>>>>>>
>>>>>>>> The only examples I found were in the share folder, where
>>>> there
>>>>>>> are
>>>>>>>> examples for collchk, graphics and logging.
>>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: mpich-discuss-bounces at mcs.anl.gov
>>>>>>>> [mailto:mpich-discuss-bounces at mcs.anl.gov] On Behalf Of Rajeev
>>>>>>>> Thakur
>>>>>>>> Sent: Wednesday, August 04, 2010 12:45 PM
>>>>>>>> To: mpich-discuss at mcs.anl.gov
>>>>>>>> Subject: Re: [mpich-discuss] cryptic (to me) error
>>>>>>>>
>>>>>>>> Not cpilog. Can you run just cpi from the mpich2/examples
>>>> directory.
>>>>>>>>
>>>>>>>> Rajeev
>>>>>>>>
>>>>>>>>
>>>>>>>> On Aug 4, 2010, at 11:37 AM, SULLIVAN David (AREVA) wrote:
>>>>>>>>
>>>>>>>>> Rajeev, Darius,
>>>>>>>>>
>>>>>>>>> Thanks for your response.
>>>>>>>>> cpi yields the following-
>>>>>>>>>
>>>>>>>>> [dfs at aramis examples_logging]$ mpiexec -host aramis -n 12
>>>> ./cpilog
>>>>
>>>>>>>>> Process 0 running on aramis Process 2 running on aramis Process
>>>> 3
>>>>>>>>> running on aramis Process 1 running on aramis Process 6 running
>>>> on
>>>>
>>>>>>>>> aramis Process 7 running on aramis Process 8 running on aramis
>>>>>>>>> Process
>>>>>>>>
>>>>>>>>> 4 running on aramis Process 5 running on aramis Process 9
>>>> running
>>>>>>>>> on
>>>>>>
>>>>>>>>> aramis Process 10 running on aramis Process 11 running on aramis
>>>>
>>>>>>>>> pi
>>>>>
>>>>>>>>> is
>>>>>>>>
>>>>>>>>> approximately 3.1415926535898762, Error is 0.0000000000000830
>>>> wall
>>>>
>>>>>>>>> clock time = 0.058131 Writing logfile....
>>>>>>>>> Enabling the Default clock synchronization...
>>>>>>>>> clog_merger.c:CLOG_Merger_init() -
>>>>>>>>> Could not open file ./cpilog.clog2 for merging!
>>>>>>>>> Backtrace of the callstack at rank 0:
>>>>>>>>> At [0]: ./cpilog(CLOG_Util_abort+0x92)[0x456326]
>>>>>>>>> At [1]: ./cpilog(CLOG_Merger_init+0x11f)[0x45db7c]
>>>>>>>>> At [2]: ./cpilog(CLOG_Converge_init+0x8e)[0x45a691]
>>>>>>>>> At [3]: ./cpilog(MPE_Finish_log+0xea)[0x4560aa]
>>>>>>>>> At [4]: ./cpilog(MPI_Finalize+0x50c)[0x4268af]
>>>>>>>>> At [5]: ./cpilog(main+0x428)[0x415963]
>>>>>>>>> At [6]:
>>>> /lib64/libc.so.6(__libc_start_main+0xf4)[0x3c1881d994]
>>>>>>>>> At [7]: ./cpilog[0x415449]
>>>>>>>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>>>>>>>>> APPLICATION TERMINATED WITH THE EXIT STRING: Terminated (signal
>>>>
>>>>>>>>> 15)
>>>>>>>>>
>>>>>>>>> So it looks like it works with some issues.
>>>>>>>>>
>>>>>>>>> When does it fail? Immediately
>>>>>>>>>
>>>>>>>>> Is there a bug? Many sucessfully use the aplication (MCNP5,
>>>>>>>>> from
>>>>>>>>> LANL) with mpi, so think that a bug there is unlikely.
>>>>>>>>>
>>>>>>>>> Core files, unfortunately reveals some ignorance on my part.
>>>> Were
>>>>>>>>> exactly should I be looking for them?
>>>>>>>>>
>>>>>>>>> Thanks again,
>>>>>>>>>
>>>>>>>>> Dave
>>>>>>>>> -----Original Message-----
>>>>>>>>> From: mpich-discuss-bounces at mcs.anl.gov
>>>>>>>>> [mailto:mpich-discuss-bounces at mcs.anl.gov] On Behalf Of Darius
>>>>>>>>> Buntinas
>>>>>>>>> Sent: Wednesday, August 04, 2010 12:19 PM
>>>>>>>>> To: mpich-discuss at mcs.anl.gov
>>>>>>>>> Subject: Re: [mpich-discuss] cryptic (to me) error
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> This error message says that two processes terminated because
>>>> they
>>>>
>>>>>>>>> were unable to communicate with another (or two other) process.
>>>>>> It's
>>>>>>>
>>>>>>>>> possible that another process died, so the others got errors
>>>>>>>>> trying
>>>>>
>>>>>>>>> to
>>>>>>>>
>>>>>>>>> communicate with them. It's also possible that there is
>>>> something
>>>>
>>>>>>>>> preventing some processes from communicating with each other.
>>>>>>>>>
>>>>>>>>> Are you able to run cpi from the examples directory with 12
>>>>>>> processes?
>>>>>>>>>
>>>>>>>>> At what point in your code does this fail? Are there any other
>>>>
>>>>>>>>> communication operations before the MPI_Comm_dup?
>>>>>>>>>
>>>>>>>>> Enable core files (add "ulimit -c unlimited" to your .bashrc or
>>>>>>>>> .tcshrc) then run your app and look for core files. If there is
>>>> a
>>>>
>>>>>>>>> bug
>>>>>>>>
>>>>>>>>> in your application that causes a process to die this might tell
>>>>
>>>>>>>>> you
>>>>>>
>>>>>>>>> which one and why.
>>>>>>>>>
>>>>>>>>> Let us know how this goes.
>>>>>>>>>
>>>>>>>>> -d
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Aug 4, 2010, at 11:03 AM, SULLIVAN David (AREVA) wrote:
>>>>>>>>>
>>>>>>>>>> Since I have had no responses, is there any other
>>>> additional
>>>>>>>>> information could I provide to solicit some direction for
>>>>>>>>> overcoming
>>>>>>
>>>>>>>>> these latest string of mpi errors?
>>>>>>>>>> Thanks,
>>>>>>>>>>
>>>>>>>>>> Dave
>>>>>>>>>>
>>>>>>>>>> From: mpich-discuss-bounces at mcs.anl.gov
>>>>>>>>>> [mailto:mpich-discuss-bounces at mcs.anl.gov] On Behalf Of
>>>> SULLIVAN
>>>>>>>>>> David F (AREVA NP INC)
>>>>>>>>>> Sent: Friday, July 23, 2010 4:29 PM
>>>>>>>>>> To: mpich-discuss at mcs.anl.gov
>>>>>>>>>> Subject: [mpich-discuss] cryptic (to me) error
>>>>>>>>>>
>>>>>>>>>> With my firewall issues firmly behind me, I have a new problem
>>>>
>>>>>>>>>> for
>>>>>
>>>>>>>>>> the
>>>>>>>>> collective wisdom. I am attempting to run a program to which the
>>>>
>>>>>>>>> response is as follows:
>>>>>>>>>> [mcnp5_1-4 at athos ~]$ mpiexec -f nodes -n 12 mcnp5.mpi i=TN04
>>>>>>>>>> o=TN04.o
>>>>>>>>
>>>>>>>>>> Fatal error in MPI_Comm_dup: Other MPI error, error stack:
>>>>>>>>>> MPI_Comm_dup(168).................:
>>>> MPI_Comm_dup(MPI_COMM_WORLD,
>>>>>>>>>> new_comm=0x7fff58edb450) failed
>>>>>>>>>> MPIR_Comm_copy(923)...............:
>>>>>>>>>> MPIR_Get_contextid(639)...........:
>>>>>>>>>> MPI_Allreduce(773)................:
>>>>>> MPI_Allreduce(sbuf=MPI_IN_PLACE,
>>>>>>>>> rbuf=0x7fff
>>>>>>>>> 58edb1a0, count=64, MPI_INT, MPI_BAND, MPI_COMM_WORLD) failed
>>>>>>>>>> MPIR_Allreduce(228)...............:
>>>>>>>>>> MPIC_Send(41).....................:
>>>>>>>>>> MPIC_Wait(513)....................:
>>>>>>>>>> MPIDI_CH3I_Progress(150)..........:
>>>>>>>>>> MPID_nem_mpich2_blocking_recv(933):
>>>>>>>>>> MPID_nem_tcp_connpoll(1709).......: Communication error Fatal
>>>>>>>>>> error
>>>>>>
>>>>>>>>>> in
>>>>>>>>>> MPI_Comm_dup: Other MPI error, error stack:
>>>>>>>>>> MPI_Comm_dup(168).................:
>>>> MPI_Comm_dup(MPI_COMM_WORLD,
>>>>>>>>> new_comm=0x7fff
>>>>>>>>> 97dca620) failed
>>>>>>>>>> MPIR_Comm_copy(923)...............:
>>>>>>>>>> MPIR_Get_contextid(639)...........:
>>>>>>>>>> MPI_Allreduce(773)................:
>>>>>> MPI_Allreduce(sbuf=MPI_IN_PLACE,
>>>>>>>>> rbuf=0x7fff
>>>>>>>>> 97dca370, count=64, MPI_INT, MPI_BAND, MPI_COMM_WORLD) failed
>>>>>>>>>> MPIR_Allreduce(289)...............:
>>>>>>>>>> MPIC_Sendrecv(161)................:
>>>>>>>>>> MPIC_Wait(513)....................:
>>>>>>>>>> MPIDI_CH3I_Progress(150)..........:
>>>>>>>>>> MPID_nem_mpich2_blocking_recv(948):
>>>>>>>>>> MPID_nem_tcp_connpoll(1709).......: Communication error Killed
>>>> by
>>>>
>>>>>>>>>> signal 2.
>>>>>>>>>> Ctrl-C caught... cleaning up processes [mpiexec at athos]
>>>>>>>>>> HYDT_dmx_deregister_fd (./tools/demux/demux.c:142): could not
>>>>>>>>>> find
>>>>>
>>>>>>>>>> fd
>>>>>>>>
>>>>>>>>>> to deregister: -2 [mpiexec at athos] HYD_pmcd_pmiserv_cleanup
>>>>>>>>>> (./pm/pmiserv/pmiserv_cb.c:401): error deregistering fd [press
>>>>
>>>>>>>>>> Ctrl-C
>>>>>>>>
>>>>>>>>>> again to force abort] APPLICATION TERMINATED WITH THE EXIT
>>>> STRING:
>>>>>>>>>> Killed (signal 9) [mcnp5_1-4 at athos ~]$ Any ideas?
>>>>>>>>>>
>>>>>>>>>> Thanks in advance,
>>>>>>>>>>
>>>>>>>>>> David Sullivan
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> AREVA NP INC
>>>>>>>>>> 400 Donald Lynch Boulevard
>>>>>>>>>> Marlborough, MA, 01752
>>>>>>>>>> Phone: (508) 573-6721
>>>>>>>>>> Fax: (434) 382-5597
>>>>>>>>>> David.Sullivan at AREVA.com
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> mpich-discuss mailing list
>>>>>>>>>> mpich-discuss at mcs.anl.gov
>>>>>>>>>> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
>>>>>>>>> _______________________________________________
>>>>>>>>> mpich-discuss mailing list
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>>>>>>>>> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
>>>>>>>>> _______________________________________________
>>>>>>>>> mpich-discuss mailing list
>>>>>>>>> mpich-discuss at mcs.anl.gov
>>>>>>>>> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> mpich-discuss mailing list
>>>>>>>> mpich-discuss at mcs.anl.gov
>>>>>>>> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
>>>>>>>> _______________________________________________
>>>>>>>> mpich-discuss mailing list
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>>>>>>>> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> mpich-discuss mailing list
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>>>>>>
>>>>>> _______________________________________________
>>>>>> mpich-discuss mailing list
>>>>>> mpich-discuss at mcs.anl.gov
>>>>>> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
>>>>>> <summary.xml>_______________________________________________
>>>>>> mpich-discuss mailing list
>>>>>> mpich-discuss at mcs.anl.gov
>>>>>> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
>>>>>
>>>>> _______________________________________________
>>>>> mpich-discuss mailing list
>>>>> mpich-discuss at mcs.anl.gov
>>>>> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
>>>>> _______________________________________________
>>>>> mpich-discuss mailing list
>>>>> mpich-discuss at mcs.anl.gov
>>>>> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
>>>>
>>>> _______________________________________________
>>>> mpich-discuss mailing list
>>>> mpich-discuss at mcs.anl.gov
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>>>>
>>>> _______________________________________________
>>>> mpich-discuss mailing list
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>>>> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
>>> _______________________________________________
>>> mpich-discuss mailing list
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>>> <summary.xml><error.txt>_______________________________________________
>>> mpich-discuss mailing list
>>> mpich-discuss at mcs.anl.gov
>>> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
>>
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