[mpich-discuss] mpich on Mac os x

Mon Jul 8 11:56:50 CDT 2013

Do you understand the different between a Fortran procedure/subroutine
and a variable value?

You cannot set an MPI communicator equal to a subroutine.  That makes
no sense and the compiler is rightfully complaining about it.

Jeff

On Mon, Jul 8, 2013 at 11:32 AM, Reem Alraddadi <raba500 at york.ac.uk> wrote:
>
> Hi Wesley,
>
> How could I do that? as I read in the internet. I have to set:
>    include "mpif.h"
>    Call MPI_COMM_FREE
>
> I found where I can set that in FLASH code ( I have attached the file) So I
> set:
>    integer, parameter :: FLASH_COMM = MPI_COMM_FREE
> but I got an error when I compile the code:
>
>     Included at Driver_abortFlash.F90:34:
>
>    integer, parameter :: FLASH_COMM = MPI_COMM_FREE
>                                    1
> Error: Symbol 'flash_comm' at (1) already has basic type of INTEGER
> make: *** [Driver_abortFlash.o] Error 1
>
> the code used   MPI_COMM_WORLD.
> So is there a way to fix that?
>
> Thanks,
> Reem
>
>
>
>> Date: Mon, 8 Jul 2013 10:25:38 -0500
>> From: Wesley Bland <wbland at mcs.anl.gov>
>> To: discuss at mpich.org
>> Subject: Re: [mpich-discuss] discuss Digest, Vol 9, Issue 13
>> Message-ID: <9A8EEBB2-72BB-429B-9368-150983B1C283 at mcs.anl.gov>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> That's the correct way to set that environment variable, but I would have
>> to agree with Pavan here. If you're running into the cap on context id's
>> (especially with so few processes) it would seem that you're creating a lot
>> of communicators that you probably don't need. Are you sure that you're
>> freeing them correctly after use?
>>
>> Wesley
>>
>> On Jul 8, 2013, at 10:05 AM, Reem Alraddadi <raba500 at york.ac.uk> wrote:
>>
>> > Hi Wesley.
>> > I wrote the following:
>> > mpirun --np 4 --env MPIR_PARAM_CTXID_EAGER_SIZE 1 ./flash4
>> > but the error still the same. Did I do it in the wrong way??
>> >
>> > Thanks,
>> > Reem
>> >
>> > Message: 5
>> > Date: Mon, 8 Jul 2013 08:14:48 -0500
>> > From: Wesley Bland <wbland at mcs.anl.gov>
>> > To: discuss at mpich.org
>> > Subject: Re: [mpich-discuss] mpich on Mac os x
>> > Message-ID: <8DC984B2-4E4B-4BFE-806E-203463A7A4E4 at mcs.anl.gov>
>> > Content-Type: text/plain; charset=iso-8859-1
>> >
>> > It seems that you're creating more communicators than MPICH can handle.
>> > It's possible that you might be able to get around this by setting the
>> > environment variable MPIR_PARAM_CTXID_EAGER_SIZE to something smaller than
>> > its default (which is 2). That frees up a few more communicators, but there
>> > is a pathological case where even with fewer communicators than the max,
>> > MPICH won't be able to agree on a new communicator id when needed. Try
>> > changing that environment variable and see if that fixes things.
>> >
>> > Wesley
>> >
>> > On Jul 8, 2013, at 5:33 AM, Reem Alraddadi <raba500 at york.ac.uk> wrote:
>> >
>> > > Hi all,
>> > > I am using mpich-3.0.4 on Mac os x version 10.7.5 to run FLASH code.
>> > > It works fine in the beginning of the run and then I got the following
>> > > error:
>> > >
>> > > Fatal error in MPI_Comm_create: Other MPI error, error stack:
>> > > MPI_Comm_create(600).................:
>> > > MPI_Comm_create(comm=0x84000002, group=0xc8001349, new_comm=0x7fff606a8614)
>> > > failed
>> > > MPI_Comm_create(577).................:
>> > > MPIR_Comm_create_intra(241)..........:
>> > > MPIR_Get_contextid(799)..............:
>> > > MPIR_Get_contextid_sparse_group(1146):  Cannot allocate context ID
>> > > because of fragmentation (169/2048 free on this process; ignore_id=0)
>> > > Fatal error in MPI_Comm_create: Other MPI error, error stack:
>> > > MPI_Comm_create(600).................:
>> > > MPI_Comm_create(comm=0x84000002, group=0xc80012b6, new_comm=0x7fff670cc614)
>> > > failed
>> > > MPI_Comm_create(577).................:
>> > > MPIR_Comm_create_intra(241)..........:
>> > > MPIR_Get_contextid(799)..............:
>> > > MPIR_Get_contextid_sparse_group(1146):  Cannot allocate context ID
>> > > because of fragmentation (316/2048 free on this process; ignore_id=0)
>> > > Fatal error in MPI_Comm_create: Other MPI error, error stack:
>> > > MPI_Comm_create(600).................:
>> > > MPI_Comm_create(comm=0x84000004, group=0xc800000e, new_comm=0x7fff629d5614)
>> > > failed
>> > > MPI_Comm_create(577).................:
>> > > MPIR_Comm_create_intra(241)..........:
>> > > MPIR_Get_contextid(799)..............:
>> > > MPIR_Get_contextid_sparse_group(1146):  Cannot allocate context ID
>> > > because of fragmentation (2020/2048 free on this process; ignore_id=0)
>> > > Fatal error in MPI_Comm_create: Other MPI error, error stack:
>> > > MPI_Comm_create(600).................:
>> > > MPI_Comm_create(comm=0x84000002, group=0xc8000020, new_comm=0x7fff639ae614)
>> > > failed
>> > > MPI_Comm_create(577).................:
>> > > MPIR_Comm_create_intra(241)..........:
>> > > MPIR_Get_contextid(799)..............:
>> > > MPIR_Get_contextid_sparse_group(1146):  Cannot allocate context ID
>> > > because of fragmentation (2002/2048 free on this process; ignore_id=0
>> > >
>> > > Is there a way to fix that ?
>> > >
>> > > Thanks,
>> > > Reem
>
>
>>
>> On Mon, Jul 8, 2013 at 9:17 AM, Pavan Balaji <balaji at mcs.anl.gov> wrote:
>> >
>> > Also make sure you are freeing unused communicators.
>> >
>> >  -- Pavan
>> >
>> > On 07/08/2013 08:14 AM, Wesley Bland wrote:
>> >>
>> >> It seems that you're creating more communicators than MPICH can handle.
>> >> It's possible that you might be able to get around this by setting the
>> >> environment variable MPIR_PARAM_CTXID_EAGER_SIZE to something smaller
>> >> than
>> >> its default (which is 2). That frees up a few more communicators, but
>> >> there
>> >> is a pathological case where even with fewer communicators than the
>> >> max,
>> >> MPICH won't be able to agree on a new communicator id when needed. Try
>> >> changing that environment variable and see if that fixes things.
>> >>
>> >> Wesley
>> >>
>> >> On Jul 8, 2013, at 5:33 AM, Reem Alraddadi <raba500 at york.ac.uk> wrote:
>> >>
>> >>> Hi all,
>> >>> I am using mpich-3.0.4 on Mac os x version 10.7.5 to run FLASH code.
>> >>> It
>> >>> works fine in the beginning of the run and then I got the following
>> >>> error:
>> >>>
>> >>> Fatal error in MPI_Comm_create: Other MPI error, error stack:
>> >>> MPI_Comm_create(600).................:
>> >>> MPI_Comm_create(comm=0x84000002,
>> >>> group=0xc8001349, new_comm=0x7fff606a8614) failed
>> >>> MPI_Comm_create(577).................:
>> >>> MPIR_Comm_create_intra(241)..........:
>> >>> MPIR_Get_contextid(799)..............:
>> >>> MPIR_Get_contextid_sparse_group(1146):  Cannot allocate context ID
>> >>> because of fragmentation (169/2048 free on this process; ignore_id=0)
>> >>> Fatal error in MPI_Comm_create: Other MPI error, error stack:
>> >>> MPI_Comm_create(600).................:
>> >>> MPI_Comm_create(comm=0x84000002,
>> >>> group=0xc80012b6, new_comm=0x7fff670cc614) failed
>> >>> MPI_Comm_create(577).................:
>> >>> MPIR_Comm_create_intra(241)..........:
>> >>> MPIR_Get_contextid(799)..............:
>> >>> MPIR_Get_contextid_sparse_group(1146):  Cannot allocate context ID
>> >>> because of fragmentation (316/2048 free on this process; ignore_id=0)
>> >>> Fatal error in MPI_Comm_create: Other MPI error, error stack:
>> >>> MPI_Comm_create(600).................:
>> >>> MPI_Comm_create(comm=0x84000004,
>> >>> group=0xc800000e, new_comm=0x7fff629d5614) failed
>> >>> MPI_Comm_create(577).................:
>> >>> MPIR_Comm_create_intra(241)..........:
>> >>> MPIR_Get_contextid(799)..............:
>> >>> MPIR_Get_contextid_sparse_group(1146):  Cannot allocate context ID
>> >>> because of fragmentation (2020/2048 free on this process; ignore_id=0)
>> >>> Fatal error in MPI_Comm_create: Other MPI error, error stack:
>> >>> MPI_Comm_create(600).................:
>> >>> MPI_Comm_create(comm=0x84000002,
>> >>> group=0xc8000020, new_comm=0x7fff639ae614) failed
>> >>> MPI_Comm_create(577).................:
>> >>> MPIR_Comm_create_intra(241)..........:
>> >>> MPIR_Get_contextid(799)..............:
>> >>> MPIR_Get_contextid_sparse_group(1146):  Cannot allocate context ID
>> >>> because of fragmentation (2002/2048 free on this process; ignore_id=0
>> >>>
>> >>> Is there a way to fix that ?
>> >>>
>> >>> Thanks,
>> >>> Reem
>> >>> _______________________________________________
>> >>> discuss mailing list     discuss at mpich.org
>> >>> To manage subscription options or unsubscribe:
>> >>> https://lists.mpich.org/mailman/listinfo/discuss
>> >>
>> >>
>> >> _______________________________________________
>> >> discuss mailing list     discuss at mpich.org
>> >> To manage subscription options or unsubscribe:
>> >> https://lists.mpich.org/mailman/listinfo/discuss
>> >>
>> >
>> > --
>> > Pavan Balaji
>> > http://www.mcs.anl.gov/~balaji
>> > _______________________________________________
>> > discuss mailing list     discuss at mpich.org
>> > To manage subscription options or unsubscribe:
>> > https://lists.mpich.org/mailman/listinfo/discuss
>>
>>
>>
>> --
>> Jeff Hammond
>> jeff.science at gmail.com
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Mon, 8 Jul 2013 16:39:03 +0100
>> From: Reem Alraddadi <raba500 at york.ac.uk>
>> To: discuss at mpich.org
>> Subject: [mpich-discuss] mpich on Mac os x
>> Message-ID:
>>
>> <CANKsntEJR0b_TA-tbdBO3fOV2O8PkwTG82a718qZPd3FnEBT3w at mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi Pavan,
>>
>> Could you explain more what do you mean by that? I am sorry I am still
>> beginner in MPICH.
>>
>> Hi Wesley,
>> apologize about my first confused reply I have forgotten to change the
>> subject. However, as I mentioned I wrote the following line:
>>
>> mpirun --np 4 --env MPIR_PARAM_CTXID_EAGER_SIZE 1 ./flash4
>>
>> I am wondering if I made any mistake here as the problem is still the same
>>
>> Thanks,
>> Reem
>>
>>
>>
>> Message: 1
>> > Date: Mon, 08 Jul 2013 09:17:00 -0500
>> > From: Pavan Balaji <balaji at mcs.anl.gov>
>> > To: discuss at mpich.org
>> > Subject: Re: [mpich-discuss] mpich on Mac os x
>> > Message-ID: <51DAC9DC.5000502 at mcs.anl.gov>
>> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> >
>> >
>> > Also make sure you are freeing unused communicators.
>> >
>> >   -- Pavan
>> >
>> > On 07/08/2013 08:14 AM, Wesley Bland wrote:
>> > > It seems that you're creating more communicators than MPICH can
>> > > handle.
>> > It's possible that you might be able to get around this by setting the
>> > environment variable MPIR_PARAM_CTXID_EAGER_SIZE to something smaller
>> > than
>> > its default (which is 2). That frees up a few more communicators, but
>> > there
>> > is a pathological case where even with fewer communicators than the max,
>> > MPICH won't be able to agree on a new communicator id when needed. Try
>> > changing that environment variable and see if that fixes things.
>> > >
>> > > Wesley
>> > >
>> > > On Jul 8, 2013, at 5:33 AM, Reem Alraddadi <raba500 at york.ac.uk> wrote:
>> > >
>> > >> Hi all,
>> > >> I am using mpich-3.0.4 on Mac os x version 10.7.5 to run FLASH code.
>> > >> It
>> > works fine in the beginning of the run and then I got the following
>> > error:
>> > >>
>> > >> Fatal error in MPI_Comm_create: Other MPI error, error stack:
>> > >> MPI_Comm_create(600).................:
>> > >> MPI_Comm_create(comm=0x84000002,
>> > group=0xc8001349, new_comm=0x7fff606a8614) failed
>> > >> MPI_Comm_create(577).................:
>> > >> MPIR_Comm_create_intra(241)..........:
>> > >> MPIR_Get_contextid(799)..............:
>> > >> MPIR_Get_contextid_sparse_group(1146):  Cannot allocate context ID
>> > because of fragmentation (169/2048 free on this process; ignore_id=0)
>> > >> Fatal error in MPI_Comm_create: Other MPI error, error stack:
>> > >> MPI_Comm_create(600).................:
>> > >> MPI_Comm_create(comm=0x84000002,
>> > group=0xc80012b6, new_comm=0x7fff670cc614) failed
>> > >> MPI_Comm_create(577).................:
>> > >> MPIR_Comm_create_intra(241)..........:
>> > >> MPIR_Get_contextid(799)..............:
>> > >> MPIR_Get_contextid_sparse_group(1146):  Cannot allocate context ID
>> > because of fragmentation (316/2048 free on this process; ignore_id=0)
>> > >> Fatal error in MPI_Comm_create: Other MPI error, error stack:
>> > >> MPI_Comm_create(600).................:
>> > >> MPI_Comm_create(comm=0x84000004,
>> > group=0xc800000e, new_comm=0x7fff629d5614) failed
>> > >> MPI_Comm_create(577).................:
>> > >> MPIR_Comm_create_intra(241)..........:
>> > >> MPIR_Get_contextid(799)..............:
>> > >> MPIR_Get_contextid_sparse_group(1146):  Cannot allocate context ID
>> > because of fragmentation (2020/2048 free on this process; ignore_id=0)
>> > >> Fatal error in MPI_Comm_create: Other MPI error, error stack:
>> > >> MPI_Comm_create(600).................:
>> > >> MPI_Comm_create(comm=0x84000002,
>> > group=0xc8000020, new_comm=0x7fff639ae614) failed
>> > >> MPI_Comm_create(577).................:
>> > >> MPIR_Comm_create_intra(241)..........:
>> > >> MPIR_Get_contextid(799)..............:
>> > >> MPIR_Get_contextid_sparse_group(1146):  Cannot allocate context ID
>> > because of fragmentation (2002/2048 free on this process; ignore_id=0
>> > >>
>> > >> Is there a way to fix that ?
>> > >>
>> > >> Thanks,
>> > >> Reem
>> > >> _______________________________________________
>> > >> discuss mailing list     discuss at mpich.org
>> > >> To manage subscription options or unsubscribe:
>> > >> https://lists.mpich.org/mailman/listinfo/discuss
>> > >
>> > > _______________________________________________
>> > > discuss mailing list     discuss at mpich.org
>> > > To manage subscription options or unsubscribe:
>> > > https://lists.mpich.org/mailman/listinfo/discuss
>> > >
>> >
>> > --
>> > Pavan Balaji
>> > http://www.mcs.anl.gov/~balaji
>> >
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>> ------------------------------
>>
>> Message: 4
>> Date: Mon, 8 Jul 2013 10:53:48 -0500
>> From: Wesley Bland <wbland at mcs.anl.gov>
>> To: discuss at mpich.org
>> Subject: Re: [mpich-discuss] mpich on Mac os x
>> Message-ID: <CEEC8B51-FFDF-40FE-BE56-E25F9C05BB27 at mcs.anl.gov>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> On Jul 8, 2013, at 10:39 AM, Reem Alraddadi <raba500 at york.ac.uk> wrote:
>>
>> > Hi Pavan,
>> >
>> > Could you explain more what do you mean by that? I am sorry I am still
>> > beginner in MPICH.
>>
>> This isn't specific to MPICH. This would be the case with any MPI
>> implementation. What he means is that you need to make sure that when you
>> are done using a communicator, you call MPI_Comm_free(communicator) so MPICH
>> can free the internal resources used by the communicator. If you never free
>> your communicators, then you will eventually run out. There is a limited
>> number of communicators available internally.
>>
>> >
>> > Hi Wesley,
>> > apologize about my first confused reply I have forgotten to change the
>> > subject. However, as I mentioned I wrote the following line:
>> >
>> > mpirun --np 4 --env MPIR_PARAM_CTXID_EAGER_SIZE 1 ./flash4
>> >
>> > I am wondering if I made any mistake here as the problem is still the
>> > same
>>
>> Yes, that's the correct way to use it, so that means your problem is
>> probably what we described above.
>>
>> >
>> > Thanks,
>> > Reem
>> >
>> >
>> >
>> > Message: 1
>> > Date: Mon, 08 Jul 2013 09:17:00 -0500
>> > From: Pavan Balaji <balaji at mcs.anl.gov>
>> > To: discuss at mpich.org
>> > Subject: Re: [mpich-discuss] mpich on Mac os x
>> > Message-ID: <51DAC9DC.5000502 at mcs.anl.gov>
>> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> >
>> >
>> > Also make sure you are freeing unused communicators.
>> >
>> >   -- Pavan
>> >
>> > On 07/08/2013 08:14 AM, Wesley Bland wrote:
>> > > It seems that you're creating more communicators than MPICH can
>> > > handle. It's possible that you might be able to get around this by setting
>> > > the environment variable MPIR_PARAM_CTXID_EAGER_SIZE to something smaller
>> > > than its default (which is 2). That frees up a few more communicators, but
>> > > there is a pathological case where even with fewer communicators than the
>> > > max, MPICH won't be able to agree on a new communicator id when needed. Try
>> > > changing that environment variable and see if that fixes things.
>> > >
>> > > Wesley
>> > >
>> > > On Jul 8, 2013, at 5:33 AM, Reem Alraddadi <raba500 at york.ac.uk> wrote:
>> > >
>> > >> Hi all,
>> > >> I am using mpich-3.0.4 on Mac os x version 10.7.5 to run FLASH code.
>> > >> It works fine in the beginning of the run and then I got the following
>> > >> error:
>> > >>
>> > >> Fatal error in MPI_Comm_create: Other MPI error, error stack:
>> > >> MPI_Comm_create(600).................:
>> > >> MPI_Comm_create(comm=0x84000002, group=0xc8001349, new_comm=0x7fff606a8614)
>> > >> failed
>> > >> MPI_Comm_create(577).................:
>> > >> MPIR_Comm_create_intra(241)..........:
>> > >> MPIR_Get_contextid(799)..............:
>> > >> MPIR_Get_contextid_sparse_group(1146):  Cannot allocate context ID
>> > >> because of fragmentation (169/2048 free on this process; ignore_id=0)
>> > >> Fatal error in MPI_Comm_create: Other MPI error, error stack:
>> > >> MPI_Comm_create(600).................:
>> > >> MPI_Comm_create(comm=0x84000002, group=0xc80012b6, new_comm=0x7fff670cc614)
>> > >> failed
>> > >> MPI_Comm_create(577).................:
>> > >> MPIR_Comm_create_intra(241)..........:
>> > >> MPIR_Get_contextid(799)..............:
>> > >> MPIR_Get_contextid_sparse_group(1146):  Cannot allocate context ID
>> > >> because of fragmentation (316/2048 free on this process; ignore_id=0)
>> > >> Fatal error in MPI_Comm_create: Other MPI error, error stack:
>> > >> MPI_Comm_create(600).................:
>> > >> MPI_Comm_create(comm=0x84000004, group=0xc800000e, new_comm=0x7fff629d5614)
>> > >> failed
>> > >> MPI_Comm_create(577).................:
>> > >> MPIR_Comm_create_intra(241)..........:
>> > >> MPIR_Get_contextid(799)..............:
>> > >> MPIR_Get_contextid_sparse_group(1146):  Cannot allocate context ID
>> > >> because of fragmentation (2020/2048 free on this process; ignore_id=0)
>> > >> Fatal error in MPI_Comm_create: Other MPI error, error stack:
>> > >> MPI_Comm_create(600).................:
>> > >> MPI_Comm_create(comm=0x84000002, group=0xc8000020, new_comm=0x7fff639ae614)
>> > >> failed
>> > >> MPI_Comm_create(577).................:
>> > >> MPIR_Comm_create_intra(241)..........:
>> > >> MPIR_Get_contextid(799)..............:
>> > >> MPIR_Get_contextid_sparse_group(1146):  Cannot allocate context ID
>> > >> because of fragmentation (2002/2048 free on this process; ignore_id=0
>> > >>
>> > >> Is there a way to fix that ?
>> > >>
>> > >> Thanks,
>> > >> Reem
>> > >> _______________________________________________
>> > >> discuss mailing list     discuss at mpich.org
>> > >> To manage subscription options or unsubscribe:
>> > >> https://lists.mpich.org/mailman/listinfo/discuss
>> > >
>> > > _______________________________________________
>> > > discuss mailing list     discuss at mpich.org
>> > > To manage subscription options or unsubscribe:
>> > > https://lists.mpich.org/mailman/listinfo/discuss
>> > >
>> >
>> > --
>> > Pavan Balaji
>> > http://www.mcs.anl.gov/~balaji
>> > _______________________________________________
>> > discuss mailing list     discuss at mpich.org
>> > To manage subscription options or unsubscribe:
>> > https://lists.mpich.org/mailman/listinfo/discuss
>>
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>>
>> _______________________________________________
>> discuss mailing list
>> discuss at mpich.org
>> https://lists.mpich.org/mailman/listinfo/discuss
>>
>> End of discuss Digest, Vol 9, Issue 15
>> **************************************
>
>
>
> _______________________________________________
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> To manage subscription options or unsubscribe:
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-- 
Jeff Hammond
jeff.science at gmail.com