June 2014 - discuss - mailman3.cels.anl.gov

Re: [mpich-discuss] mpirun not running in batch mode.
by Gilles Gouaillardet 13 Jun '14

13 Jun '14

Francisco, i cannot access to the vernote.com web site :-( anyway, you can try to add the following two lines : export PATH=/usr/local/mpich2-1.0.5/bin:$PATH export LD_LIBRARY_PATH=/usr/local/mpich2-1.0.5/lib:$LD_LIBRARY_PATH at the beginning of your cron script and try again Cheers, Gilles On 2014/06/13 18:44, Francisco Pastor wrote: > I tried what you said and it seems you are right about environment. In > the case run from crontab there is an error message telling mpirun is > not found and a warning: > > "ldd: faltan los ficheros de argumentos /(missing argument files)"/ > > You can see full output of shell, at and crontab in: > > https://www.evernote.com/shard/s162/sh/641d8db6-9252-49f5-b7d7-3592e0591c2f… > > > Should I add export PATH=/usr/local/mpich2-1.0.5 to the script? I'm > gonna try. What about the ldd message?

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Re: [mpich-discuss] mpirun not running in batch mode.
by Francisco Pastor 13 Jun '14

13 Jun '14

Hi Gilles As I'm using mpich2-1.0.5 I just need an mpd.hosts file in the directory I'm running the executable. Yesterday I installed mpich3.1 and compiled my application but running issued an error about a shared library so I went back to mpich2. Maybe I should upgrade. Going back to mpich2, yes I can run mpirun -n 40 hostname > log.hostname both from shell and at, yielding names of the five nodes. But if run from crontab log.hostname is empty (0 size). Maybe the problem is crontab and not application related. Yes, I can ssh passwordless between every node in the cluster Yes, I run /home/meteo/RAMS/SCRIPTS/RAMS_operatiu.bash and "mpirun -n 40 ./rams60" from the shell and output is fine, running rams60 processes in all nodes. Thanks for your interest and help El 13/06/2014 4:01, Gilles Gouaillardet escribiï¿½: > Francisco, > > this is fine, i just wanted to double check you were not using a > machinefile the wrong way. > > your initial request was : >> If the script that runs the model is scheduled with cron it just >> starts processes on the main node but not in the rest of the cluster >> nodes. > and from what i can read, you are not using any machinefile. > how do you expect your job run on all the cluster nodes if you do not > have a machinefile ? > > can you run > $ruta_mpi/mpirun -n 40 hostname > both from shell and crontab > > which nodes are used in both cases ? > > > by the way, can you ssh passwordless on all the nodes from where the > cron is ran ? > passwordless means you do not need to enter any password and/or > passphrase nor "save" your passphase via ssh-agent. > > and could you confirm > /home/meteo/RAMS/SCRIPTS/RAMS_operatiu.bash < /dev/null > > works fine from the shell ? > > Cheers, > > Gilles > > On 2014/06/12 21:37, Francisco Pastor wrote: >> RAMSIN.operatiu is not machinefile. It is a configuration file read by >> ./rams60. >> >> May this be causing a conflict? Does mpirun try to read RAMSIN.operatiu? >> > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > > -- ----------- Dr. Francisco Pastor Meteorology department, Instituto Universitario CEAM-UMH http://www.ceam.es ----------- Mendeley profile: http://www.mendeley.com/profiles/francisco-pastor1/ Google Scholar: http://scholar.google.com/citations?user=V3mmCdkAAAAJ&hl=es Researcher ID: http://www.researcherid.com/rid/B-8331-2008 Cosis profile: http://www.cosis.net/profile/francisco.pastor ----------- mail: paco(a)ceam.es skype: paco.pastor.guzman ----------- Parque Tecnologico, C/ Charles R. Darwin, 14 46980 PATERNA (Valencia), Spain Tlf. 96 131 82 27 - Fax. 96 131 81 90 --------------------------------------------------------------------- Este mensaje y los ficheros anexos son confidenciales. Los mismos contienen informaciï¿½n reservada de la empresa que no puede ser difundida. Si usted ha recibido este correo por error, tenga la amabilidad de eliminarlo de su sistema y avisar al remitente mediante reenvï¿½o a su direcciï¿½n electrï¿½nica; no deberï¿½ copiar el mensaje ni divulgar su contenido a ninguna persona. Su direcciï¿½n de correo electrï¿½nico junto a sus datos personales forman parte de un fichero titularidad de la Fundaciï¿½n de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterrï¿½neo - CEAM, con CIF: G-46957213, cuya finalidad es la de mantener el contacto con Ud. De acuerdo con la Ley Orgï¿½nica 15/1999, usted puede ejercitar sus derechos de acceso, rectificaciï¿½n, cancelaciï¿½n y, en su caso, oposiciï¿½n enviando una solicitud por escrito, acompaï¿½ada de una fotocopia de su DNI dirigida a: Fundaciï¿½n de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterrï¿½neo - CEAM. C/ Charles R. Darwin, 14. Parque Tecnolï¿½gico.46980 PATERNA (Valencia). This message and the attached files are confidential. They contain reserved information belonging to our centre and are not to be broadcast. If you have received this email by mistake, please delete it from your system and alert the sender by returning it to his/her email address. You must not copy or divulge the contents of the message to anyone. Your email address and personal data are included in a file belonging to the Fundaciï¿½n de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterrï¿½neo - CEAM, con CIF: G-46957213. The purpose of this file is to allow us to keep in contact with you. In accordance with Organic Law 15/1999, you are permitted to access, rectify, cancel or oppose the contents of this file by submitting a written request, accompanied by a photocopy of your DNI, to: Fundaciï¿½n de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterrï¿½neo - CEAM. C/ Charles R. Darwin, 14. Parque Tecnolï¿½gico.46980 PATERNA (Valencia).

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Re: [mpich-discuss] mpirun not running in batch mode.
by Gilles Gouaillardet 13 Jun '14

13 Jun '14

Hi Francisco, On 2014/06/13 16:28, Francisco Pastor wrote: > As I'm using mpich2-1.0.5 I just need an mpd.hosts file in the > directory I'm running the executable. Yesterday I installed mpich3.1 > and compiled my application but running issued an error about a shared > library so I went back to mpich2. Maybe I should upgrade. > > Going back to mpich2, yes I can run > > mpirun -n 40 hostname > log.hostname > > both from shell and at, yielding names of the five nodes. > > But if run from crontab log.hostname is empty (0 size). Maybe the > problem is crontab and not application related. hummm this is likely due to the environment not being set within cron. can you run the following script from both shell and crontab and look for the differences ? pwd > log.hostname 2>&1 which mpirun >> log.hostname 2>&1 ldd `which mpirun` >> log.hostname 2>&1 ulimit -a >> log.hostname 2>&1 mpirun -n 40 hostname >> log.hostname 2>&1 Cheers, Gilles

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Re: [mpich-discuss] mpirun not running in batch mode.
by Gilles Gouaillardet 12 Jun '14

12 Jun '14

Francisco, this is fine, i just wanted to double check you were not using a machinefile the wrong way. your initial request was : > If the script that runs the model is scheduled with cron it just > starts processes on the main node but not in the rest of the cluster > nodes. and from what i can read, you are not using any machinefile. how do you expect your job run on all the cluster nodes if you do not have a machinefile ? can you run $ruta_mpi/mpirun -n 40 hostname both from shell and crontab which nodes are used in both cases ? by the way, can you ssh passwordless on all the nodes from where the cron is ran ? passwordless means you do not need to enter any password and/or passphrase nor "save" your passphase via ssh-agent. and could you confirm /home/meteo/RAMS/SCRIPTS/RAMS_operatiu.bash < /dev/null works fine from the shell ? Cheers, Gilles On 2014/06/12 21:37, Francisco Pastor wrote: > RAMSIN.operatiu is not machinefile. It is a configuration file read by > ./rams60. > > May this be causing a conflict? Does mpirun try to read RAMSIN.operatiu? >

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Issue with MPI_IALLTOALL on Cray XE6
by Rattermann . Dale 12 Jun '14

12 Jun '14

Hi, I'm not sure if anyone can help me with this question but I'll ask anyway. I'm working on optimizing a code that utilizes MPI on a Cray XE6. In this code there is a subroutine that calls MPI_ALLTOALL 16 different times. I changed this code so that non-blocking MPI_IALLTOALLs were used instead so that computation could be overlapped with communication, but found that it actually slowed the code down quite considerably. I wrote a little test program in fortran (that I have attached below) in order to time the two different scenarios. I've tried using both the cray-mpich/6.0.0 and cray-mpich/6.3.0 modules. I've noticed two things by running this code: 1) MPI_IALLTOALL and MPI_WAIT run slower than MPI_ALLTOALL on the Cray… even when computation and communication are overlapped using the former 2) MPI_ALLTOALL runs very slow the first time it is called (this can be seen by commenting out the MPI_ALLTOALL call on lines 26 and 27 in the attached code and compiling and running) I'm using an interactive batch session on Garnet with 2 compute nodes (64 cores total). I've compiled and run the code using the following: ftn mpi_test.f aprun -n 64 ./a.out 6400000 Here is an example of results I get while running with lines 26 and 27 uncommented: nratter@batch04-wlm:~/temp/mpi_test> make clean; make; aprun -n 64 ./a.out 6400000 rm a.out ftn mpi_test.f 0 : dt for MPI_ALLTOALL section = 0.9902300834655762 0 : dt for MPI_IALLTOALL section = 1.116391181945801 And here is an example of results I get while running with lines 26 and 27 commented out: nratter@batch04-wlm:~/temp/mpi_test> make clean; make; aprun -n 64 ./a.out 6400000 rm a.out ftn mpi_test.f 0 : dt for MPI_ALLTOALL section = 2.331636905670166 0 : dt for MPI_IALLTOALL section = 1.070204973220825 Does anyone know of a way to improve both the efficiency of MPI_IALLTOALL/MPI_WAIT and preventing the first call to MPI_ALLTOALL from taking so long? In terms of priority, I am much more interested in improving the non-blocking communications. I've tried many different combinations of environment variables with no success. Thanks for your time… I'm hoping someone can help here. Thanks, Nick Rattermann ------------------------- program hello_world implicit none include 'mpif.h' integer ierr, num_procs, my_id,rqst(2),cnt,i,N,maxnum real*8,dimension(:),allocatable :: a,atemp,b,btemp, > c,ctemp,d,dtemp,e,f character(len=100) :: arg double precision :: t1,t2 CALL GETARG(1,arg) !Grab the 2nd command line argument ! and store it in the temporary variable ! 'arg' read(arg,*) maxnum !Now convert string to integer allocate(a(maxnum),atemp(maxnum),b(maxnum),btemp(maxnum), > c(maxnum),ctemp(maxnum),d(maxnum),dtemp(maxnum), > e(maxnum),f(maxnum)) call MPI_INIT ( ierr ) ! find out MY process ID, and how many processes were started. call MPI_COMM_RANK (MPI_COMM_WORLD, my_id, ierr) call MPI_COMM_SIZE (MPI_COMM_WORLD, num_procs, ierr) call MPI_ALLTOALL(c,maxnum/num_procs,MPI_REAL8,ctemp, > MAXNUM/num_procs,MPI_REAL8,MPI_COMM_WORLD,ierr) !- MPI_ALLTOALL SECTION a = 1. atemp = 0. b = 2. btemp = 0. call MPI_BARRIER(MPI_COMM_WORLD,ierr) t1 = MPI_WTIME() call MPI_ALLTOALL(a,maxnum/num_procs,MPI_REAL8,atemp, > MAXNUM/num_procs,MPI_REAL8,MPI_COMM_WORLD,ierr) call MPI_ALLTOALL(b,maxnum/num_procs,MPI_REAL8,btemp, > MAXNUM/num_procs,MPI_REAL8,MPI_COMM_WORLD,ierr) do i=1,maxnum e(i) = real(i) end do cnt = 0 do i=1,maxnum if (atemp(i) .ne. 1.) cnt = cnt + 1 end do if (cnt .ne. 0) print *,my_id,": ATEMP NOT EQUAL TO 1!!!" cnt = 0 do i=1,maxnum if (btemp(i) .ne. 2.) cnt = cnt + 1 end do if (cnt .ne. 0) print *,my_id,": BTEMP NOT EQUAL TO 2!!!" t2 = MPI_WTIME() if (my_id == 0) print*,my_id,": dt for MPI_ALLTOALL section = ", > t2-t1 !- MPI_IALLTOALL SECTION c = 1. ctemp = 0. d = 2. dtemp = 0. call MPI_BARRIER(MPI_COMM_WORLD,ierr) t1 = MPI_WTIME() call MPI_IALLTOALL(c,maxnum/num_procs,MPI_REAL8,ctemp, > MAXNUM/num_procs,MPI_REAL8,MPI_COMM_WORLD,rqst(1),ierr) call MPI_IALLTOALL(d,maxnum/num_procs,MPI_REAL8,dtemp, > MAXNUM/num_procs,MPI_REAL8,MPI_COMM_WORLD,rqst(2),ierr) do i=1,maxnum f(i) = real(i) end do call MPI_WAIT(rqst(1),MPI_STATUS_IGNORE,ierr) cnt = 0 do i=1,maxnum if (ctemp(i) .ne. 1.) cnt = cnt + 1 end do if (cnt .ne. 0) print *,my_id,": ATEMP NOT EQUAL TO 1!!!" call MPI_WAIT(rqst(2),MPI_STATUS_IGNORE,ierr) cnt = 0 do i=1,maxnum if (dtemp(i) .ne. 2.) cnt = cnt + 1 end do if (cnt .ne. 0) print *,my_id,": BTEMP NOT EQUAL TO 2!!!" t2 = MPI_WTIME() if (my_id == 0) print*,my_id,": dt for MPI_IALLTOALL section = " > ,t2-t1 call MPI_FINALIZE ( ierr ) deallocate(a,atemp,b,btemp,c,ctemp,d,dtemp,e,f) end ________________________________ This electronic message transmission and any attachments that accompany it contain information from DRC® (Dynamics Research Corporation) or its subsidiaries, or the intended recipient, which is privileged, proprietary, business confidential, or otherwise protected from disclosure and is the exclusive property of DRC and/or the intended recipient. 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Re: [mpich-discuss] Compiling Intel MPI Benchmark (for mpich2)
by "Antonio J. Peña" 12 Jun '14

12 Jun '14

What MPICH version are you using? You may be using a too old one which does not incorporate that functionality. You can download the latest one (3.1.1) from www.mpich.org. Antonio On 06/12/2014 09:25 AM, Klaus Philip wrote: > > Hi, > > This is my first post to this mailing list. > > After working two month with mpich2 I decided to try the Intel MPI > Benchmark. > > The strange thing is, that at compiling the sources, I get an linker > error when mpicc wants to compile the files for the asynchronous > communication. > > Further I can use the asynchronous function in my self-written > programs without any problems or errors. > > *_So this is the command I execute:_* > > /home/rpimpi/mpich2-install/bin/mpicc -O0 -DNBC IMB.c IMB_declare.c > IMB_init.c IMB_mem_manager.c IMB_parse_name_nbc.c IMB_benchlist.c > IMB_strgs.c IMB_err_handler.c IMB_g_info.c IMB_warm_up.c IMB_output.c > IMB_allreduce.c IMB_reduce_scatter.c IMB_reduce.c IMB_bcast.c > IMB_barrier.c IMB_allgather.c IMB_allgatherv.c IMB_gather.c > IMB_gatherv.c IMB_scatter.c IMB_scatterv.c IMB_alltoall.c > IMB_alltoallv.c IMB_sendrecv.c IMB_init_transfer.c IMB_chk_diff.c > IMB_cpu_exploit.c -o IMB-NBC > > *_And this is the output I get:_* > > /tmp/ccEEnyN2.o: In function `IMB_iallreduce': > > IMB_allreduce.c:(.text+0x1bc): undefined reference to `MPI_Iallreduce' > > /tmp/ccEEnyN2.o: In function `IMB_iallreduce_pure': > > IMB_allreduce.c:(.text+0x438): undefined reference to `MPI_Iallreduce' > > /tmp/cc3xs7IY.o: In function `IMB_ireduce_scatter': > > IMB_reduce_scatter.c:(.text+0x190): undefined reference to > `MPI_Ireduce_scatter' > > /tmp/cc3xs7IY.o: In function `IMB_ireduce_scatter_pure': > > IMB_reduce_scatter.c:(.text+0x4a8): undefined reference to > `MPI_Ireduce_scatter' > > /tmp/ccnDYI6U.o: In function `IMB_ireduce': > > IMB_reduce.c:(.text+0x1e4): undefined reference to `MPI_Ireduce' > > /tmp/ccnDYI6U.o: In function `IMB_ireduce_pure': > > IMB_reduce.c:(.text+0x488): undefined reference to `MPI_Ireduce' > > /tmp/ccsnt9EQ.o: In function `IMB_ibcast': > > IMB_bcast.c:(.text+0x1c0): undefined reference to `MPI_Ibcast' > > /tmp/ccsnt9EQ.o: In function `IMB_ibcast_pure': > > IMB_bcast.c:(.text+0x46c): undefined reference to `MPI_Ibcast' > > /tmp/ccW45dyI.o: In function `IMB_ibarrier': > > IMB_barrier.c:(.text+0xf0): undefined reference to `MPI_Ibarrier' > > /tmp/ccW45dyI.o: In function `IMB_ibarrier_pure': > > IMB_barrier.c:(.text+0x29c): undefined reference to `MPI_Ibarrier' > > /tmp/cc5Jqe5y.o: In function `IMB_iallgather': > > IMB_allgather.c:(.text+0x208): undefined reference to `MPI_Iallgather' > > /tmp/cc5Jqe5y.o: In function `IMB_iallgather_pure': > > IMB_allgather.c:(.text+0x4c4): undefined reference to `MPI_Iallgather' > > /tmp/cc1sWF8r.o: In function `IMB_iallgatherv': > > IMB_allgatherv.c:(.text+0x218): undefined reference to `MPI_Iallgatherv' > > /tmp/cc1sWF8r.o: In function `IMB_iallgatherv_pure': > > IMB_allgatherv.c:(.text+0x550): undefined reference to `MPI_Iallgatherv' > > /tmp/cce30p6o.o: In function `IMB_igather': > > IMB_gather.c:(.text+0x230): undefined reference to `MPI_Igather' > > /tmp/cce30p6o.o: In function `IMB_igather_pure': > > IMB_gather.c:(.text+0x514): undefined reference to `MPI_Igather' > > /tmp/ccQygcKr.o: In function `IMB_igatherv': > > IMB_gatherv.c:(.text+0x240): undefined reference to `MPI_Igatherv' > > /tmp/ccQygcKr.o: In function `IMB_igatherv_pure': > > IMB_gatherv.c:(.text+0x5a0): undefined reference to `MPI_Igatherv' > > /tmp/ccNpVNux.o: In function `IMB_iscatter': > > IMB_scatter.c:(.text+0x230): undefined reference to `MPI_Iscatter' > > /tmp/ccNpVNux.o: In function `IMB_iscatter_pure': > > IMB_scatter.c:(.text+0x514): undefined reference to `MPI_Iscatter' > > /tmp/ccRgsSLD.o: In function `IMB_iscatterv': > > IMB_scatterv.c:(.text+0x244): undefined reference to `MPI_Iscatterv' > > /tmp/ccRgsSLD.o: In function `IMB_iscatterv_pure': > > IMB_scatterv.c:(.text+0x5ac): undefined reference to `MPI_Iscatterv' > > /tmp/cceoMEjN.o: In function `IMB_ialltoall': > > IMB_alltoall.c:(.text+0x208): undefined reference to `MPI_Ialltoall' > > /tmp/cceoMEjN.o: In function `IMB_ialltoall_pure': > > IMB_alltoall.c:(.text+0x4c4): undefined reference to `MPI_Ialltoall' > > /tmp/ccbHoHAQ.o: In function `IMB_ialltoallv': > > IMB_alltoallv.c:(.text+0x230): undefined reference to `MPI_Ialltoallv' > > /tmp/ccbHoHAQ.o: In function `IMB_ialltoallv_pure': > > IMB_alltoallv.c:(.text+0x5c0): undefined reference to `MPI_Ialltoallv' > > collect2: ld returned 1 exit status > > I hope someone of you can help me concerning this problem. > > Greetings, > > Philip > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- Antonio J. Peï¿½a Postdoctoral Appointee Mathematics and Computer Science Division Argonne National Laboratory 9700 South Cass Avenue, Bldg. 240, Of. 3148 Argonne, IL 60439-4847 apenya(a)mcs.anl.gov www.mcs.anl.gov/~apenya

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Compiling Intel MPI Benchmark (for mpich2)
by Klaus Philip 12 Jun '14

12 Jun '14

Hi, This is my first post to this mailing list. After working two month with mpich2 I decided to try the Intel MPI Benchmark. The strange thing is, that at compiling the sources, I get an linker error when mpicc wants to compile the files for the asynchronous communication. Further I can use the asynchronous function in my self-written programs without any problems or errors. So this is the command I execute: /home/rpimpi/mpich2-install/bin/mpicc -O0 -DNBC IMB.c IMB_declare.c IMB_init.c IMB_mem_manager.c IMB_parse_name_nbc.c IMB_benchlist.c IMB_strgs.c IMB_err_handler.c IMB_g_info.c IMB_warm_up.c IMB_output.c IMB_allreduce.c IMB_reduce_scatter.c IMB_reduce.c IMB_bcast.c IMB_barrier.c IMB_allgather.c IMB_allgatherv.c IMB_gather.c IMB_gatherv.c IMB_scatter.c IMB_scatterv.c IMB_alltoall.c IMB_alltoallv.c IMB_sendrecv.c IMB_init_transfer.c IMB_chk_diff.c IMB_cpu_exploit.c -o IMB-NBC And this is the output I get: /tmp/ccEEnyN2.o: In function `IMB_iallreduce': IMB_allreduce.c:(.text+0x1bc): undefined reference to `MPI_Iallreduce' /tmp/ccEEnyN2.o: In function `IMB_iallreduce_pure': IMB_allreduce.c:(.text+0x438): undefined reference to `MPI_Iallreduce' /tmp/cc3xs7IY.o: In function `IMB_ireduce_scatter': IMB_reduce_scatter.c:(.text+0x190): undefined reference to `MPI_Ireduce_scatter' /tmp/cc3xs7IY.o: In function `IMB_ireduce_scatter_pure': IMB_reduce_scatter.c:(.text+0x4a8): undefined reference to `MPI_Ireduce_scatter' /tmp/ccnDYI6U.o: In function `IMB_ireduce': IMB_reduce.c:(.text+0x1e4): undefined reference to `MPI_Ireduce' /tmp/ccnDYI6U.o: In function `IMB_ireduce_pure': IMB_reduce.c:(.text+0x488): undefined reference to `MPI_Ireduce' /tmp/ccsnt9EQ.o: In function `IMB_ibcast': IMB_bcast.c:(.text+0x1c0): undefined reference to `MPI_Ibcast' /tmp/ccsnt9EQ.o: In function `IMB_ibcast_pure': IMB_bcast.c:(.text+0x46c): undefined reference to `MPI_Ibcast' /tmp/ccW45dyI.o: In function `IMB_ibarrier': IMB_barrier.c:(.text+0xf0): undefined reference to `MPI_Ibarrier' /tmp/ccW45dyI.o: In function `IMB_ibarrier_pure': IMB_barrier.c:(.text+0x29c): undefined reference to `MPI_Ibarrier' /tmp/cc5Jqe5y.o: In function `IMB_iallgather': IMB_allgather.c:(.text+0x208): undefined reference to `MPI_Iallgather' /tmp/cc5Jqe5y.o: In function `IMB_iallgather_pure': IMB_allgather.c:(.text+0x4c4): undefined reference to `MPI_Iallgather' /tmp/cc1sWF8r.o: In function `IMB_iallgatherv': IMB_allgatherv.c:(.text+0x218): undefined reference to `MPI_Iallgatherv' /tmp/cc1sWF8r.o: In function `IMB_iallgatherv_pure': IMB_allgatherv.c:(.text+0x550): undefined reference to `MPI_Iallgatherv' /tmp/cce30p6o.o: In function `IMB_igather': IMB_gather.c:(.text+0x230): undefined reference to `MPI_Igather' /tmp/cce30p6o.o: In function `IMB_igather_pure': IMB_gather.c:(.text+0x514): undefined reference to `MPI_Igather' /tmp/ccQygcKr.o: In function `IMB_igatherv': IMB_gatherv.c:(.text+0x240): undefined reference to `MPI_Igatherv' /tmp/ccQygcKr.o: In function `IMB_igatherv_pure': IMB_gatherv.c:(.text+0x5a0): undefined reference to `MPI_Igatherv' /tmp/ccNpVNux.o: In function `IMB_iscatter': IMB_scatter.c:(.text+0x230): undefined reference to `MPI_Iscatter' /tmp/ccNpVNux.o: In function `IMB_iscatter_pure': IMB_scatter.c:(.text+0x514): undefined reference to `MPI_Iscatter' /tmp/ccRgsSLD.o: In function `IMB_iscatterv': IMB_scatterv.c:(.text+0x244): undefined reference to `MPI_Iscatterv' /tmp/ccRgsSLD.o: In function `IMB_iscatterv_pure': IMB_scatterv.c:(.text+0x5ac): undefined reference to `MPI_Iscatterv' /tmp/cceoMEjN.o: In function `IMB_ialltoall': IMB_alltoall.c:(.text+0x208): undefined reference to `MPI_Ialltoall' /tmp/cceoMEjN.o: In function `IMB_ialltoall_pure': IMB_alltoall.c:(.text+0x4c4): undefined reference to `MPI_Ialltoall' /tmp/ccbHoHAQ.o: In function `IMB_ialltoallv': IMB_alltoallv.c:(.text+0x230): undefined reference to `MPI_Ialltoallv' /tmp/ccbHoHAQ.o: In function `IMB_ialltoallv_pure': IMB_alltoallv.c:(.text+0x5c0): undefined reference to `MPI_Ialltoallv' collect2: ld returned 1 exit status I hope someone of you can help me concerning this problem. Greetings, Philip

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Re: [mpich-discuss] mpirun not running in batch mode.
by Francisco Pastor 12 Jun '14

12 Jun '14

Hi Gilles RAMSIN.operatiu is not machinefile. It is a configuration file read by ./rams60. May this be causing a conflict? Does mpirun try to read RAMSIN.operatiu? El 12/06/2014 11:38, Gilles Gouaillardet escribiï¿½: > Francisco, > > from the shell, can you try to run > /home/meteo/RAMS/SCRIPTS/RAMS_operatiu.bash < /dev/null > and confirm everything works as expected ? > > also, i cannot see any machinefile. > is /home/meteo/RAMS/RUN/RAMSIN.operatiu your machinefile ? > if yes, can you replace > > $ruta_mpi/mpirun -n 40 ./rams60 -f /home/meteo/RAMS/RUN/RAMSIN.operatiu >> $log-INITIAL-$hoy-$horasim > with > > $ruta_mpi/mpirun -n 40 -f /home/meteo/RAMS/RUN/RAMSIN.operatiu ./rams60 >> $log-INITIAL-$hoy-$horasim > and give it a try (both from shell and crontab) > > Cheers, > > Gilles > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > > -- ----------- Dr. Francisco Pastor Meteorology department, Instituto Universitario CEAM-UMH http://www.ceam.es ----------- Mendeley profile: http://www.mendeley.com/profiles/francisco-pastor1/ Google Scholar: http://scholar.google.com/citations?user=V3mmCdkAAAAJ&hl=es Researcher ID: http://www.researcherid.com/rid/B-8331-2008 Cosis profile: http://www.cosis.net/profile/francisco.pastor ----------- mail: paco(a)ceam.es skype: paco.pastor.guzman ----------- Parque Tecnologico, C/ Charles R. Darwin, 14 46980 PATERNA (Valencia), Spain Tlf. 96 131 82 27 - Fax. 96 131 81 90 --------------------------------------------------------------------- Este mensaje y los ficheros anexos son confidenciales. Los mismos contienen informaciï¿½n reservada de la empresa que no puede ser difundida. Si usted ha recibido este correo por error, tenga la amabilidad de eliminarlo de su sistema y avisar al remitente mediante reenvï¿½o a su direcciï¿½n electrï¿½nica; no deberï¿½ copiar el mensaje ni divulgar su contenido a ninguna persona. Su direcciï¿½n de correo electrï¿½nico junto a sus datos personales forman parte de un fichero titularidad de la Fundaciï¿½n de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterrï¿½neo - CEAM, con CIF: G-46957213, cuya finalidad es la de mantener el contacto con Ud. De acuerdo con la Ley Orgï¿½nica 15/1999, usted puede ejercitar sus derechos de acceso, rectificaciï¿½n, cancelaciï¿½n y, en su caso, oposiciï¿½n enviando una solicitud por escrito, acompaï¿½ada de una fotocopia de su DNI dirigida a: Fundaciï¿½n de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterrï¿½neo - CEAM. C/ Charles R. Darwin, 14. Parque Tecnolï¿½gico.46980 PATERNA (Valencia). This message and the attached files are confidential. They contain reserved information belonging to our centre and are not to be broadcast. If you have received this email by mistake, please delete it from your system and alert the sender by returning it to his/her email address. You must not copy or divulge the contents of the message to anyone. Your email address and personal data are included in a file belonging to the Fundaciï¿½n de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterrï¿½neo - CEAM, con CIF: G-46957213. The purpose of this file is to allow us to keep in contact with you. In accordance with Organic Law 15/1999, you are permitted to access, rectify, cancel or oppose the contents of this file by submitting a written request, accompanied by a photocopy of your DNI, to: Fundaciï¿½n de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterrï¿½neo - CEAM. C/ Charles R. Darwin, 14. Parque Tecnolï¿½gico.46980 PATERNA (Valencia).

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Re: [mpich-discuss] mpirun not running in batch mode.
by Gilles Gouaillardet 12 Jun '14

12 Jun '14

Francisco, from the shell, can you try to run /home/meteo/RAMS/SCRIPTS/RAMS_operatiu.bash < /dev/null and confirm everything works as expected ? also, i cannot see any machinefile. is /home/meteo/RAMS/RUN/RAMSIN.operatiu your machinefile ? if yes, can you replace $ruta_mpi/mpirun -n 40 ./rams60 -f /home/meteo/RAMS/RUN/RAMSIN.operatiu > $log-INITIAL-$hoy-$horasim with $ruta_mpi/mpirun -n 40 -f /home/meteo/RAMS/RUN/RAMSIN.operatiu ./rams60 > $log-INITIAL-$hoy-$horasim and give it a try (both from shell and crontab) Cheers, Gilles

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Re: [mpich-discuss] failures of make testing
by Rajeev Thakur 12 Jun '14

12 Jun '14

You can ignore them. Rajeev On Jun 12, 2014, at 3:06 AM, Xaver Gerster <torreeger(a)yahoo.com> wrote: > Hi, > on a fresh install of version 3.1.1 I get these two failures in 'make > testing'. > > Any clue if they are relevant, and if so how to fix them? > > Thanks, > Xaver > > not ok 56 - ./coll/bcast2 10 > --- > Directory: ./coll > File: bcast2 > Num-procs: 10 > Date: "Thu Jun 12 08:12:18 2014" > ... > ## Test output (expected 'No Errors'): > ## [mpiexec@xxx] APPLICATION TIMED OUT > ## [proxy:0:0@xxx] HYD_pmcd_pmip_control_cmd_cb > (pm/pmiserv/pmip_cb.c:885): assert (!closed) failed > ## [proxy:0:0@xxx] HYDT_dmxu_poll_wait_for_event > (tools/demux/demux_poll.c:76): callback returned error status > ## [proxy:0:0@xxx] main (pm/pmiserv/pmip.c:206): demux engine error > waiting for event > ## [mpiexec@xxx] HYDT_bscu_wait_for_completion > (tools/bootstrap/utils/bscu_wait.c:76): one of the processes terminated > badly; aborting > ## [mpiexec@xxx] HYDT_bsci_wait_for_completion > (tools/bootstrap/src/bsci_wait.c:23): launcher returned error waiting > for completion > ## [mpiexec@xxx] HYD_pmci_wait_for_completion > (pm/pmiserv/pmiserv_pmci.c:189): launcher returned error waiting for > completion > ## [mpiexec@xxx] main (ui/mpich/mpiexec.c:344): process manager error > waiting for completion > > not ok 290 - ./pt2pt/sendflood 8 > --- > Directory: ./pt2pt > File: sendflood > Num-procs: 8 > Date: "Thu Jun 12 08:40:10 2014" > ... > ## Test output (expected 'No Errors'): > ## [mpiexec@xxx] APPLICATION TIMED OUT > ## [proxy:0:0@xxx] HYD_pmcd_pmip_control_cmd_cb > (pm/pmiserv/pmip_cb.c:885): assert (!closed) failed > ## [proxy:0:0@xxx] HYDT_dmxu_poll_wait_for_event > (tools/demux/demux_poll.c:76): callback returned error status > ## [proxy:0:0@xxx] main (pm/pmiserv/pmip.c:206): demux engine error > waiting for event > ## [mpiexec@xxx] HYDT_bscu_wait_for_completion > (tools/bootstrap/utils/bscu_wait.c:76): one of the processes terminated > badly; aborting > ## [mpiexec@xxx] HYDT_bsci_wait_for_completion > (tools/bootstrap/src/bsci_wait.c:23): launcher returned error waiting > for completion > ## [mpiexec@xxx] HYD_pmci_wait_for_completion > (pm/pmiserv/pmiserv_pmci.c:189): launcher returned error waiting for > completion > ## [mpiexec@xxx] main (ui/mpich/mpiexec.c:344): process manager error > waiting for completion > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

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