December 2012 - discuss - mailman3.cels.anl.gov

Hangup or stall at MPI_INIT
by Ryan Crocker 06 Dec '12

06 Dec '12

Hi all, I'm having a problem with hangups or some sort of stall. Basically the program will keep running, or look as it if is on the cluster i'm running on (i've noticed this issue on multiple clusters actually), But nothing is happening. When i have every processor print out they all do right before MPI_INIT and not after. I counted the files and all the processors are entering the call. What makes it even more odd is that the same exact simulation will run if i decrease the number of nodes/cores i'm using, i.e. i'll run on 96 cores (or more) and moving to 72 my program will run without issue. I'm using the latest gcc compiler set with the latest version of MPICH2 configured with: '--with-pbs=/PBS' '--with-default-comm=pmi' '--enable-pbspro-helper' 'CC=gcc' 'LDFLAGS=-lpthread' 'CPPFLAGS=-fpic' I've changed to the intel/mpich2 compiler set and have not had the same problem. I have no idea what this issue could be and have had little luck finding an answer with stackoverflow or google searches any help would be much appreciated. Also, hit me up for any more information you'd need to help. Thanks, My flow solver is written in fortran and here are the subroutines leading up to the MPI_INIT call, and the whole flow solver is compiled with '-O3 -ffree-line-length-none' : ! ====================================== ! program main call main_init call simulation_run call main_stop end program main ! ====================================== ! subroutine main_init use string implicit none character(len=str_medium) :: input_name call parallel_init ! Initialize the random number generator call random_init ! Parse the input file call parser_init input_name='input' call parser_parsefile(input_name) ! Geometry initialization call geometry_init ! Data initialization call data_init ! Simulation initialization call simulation_init return end subroutine main_init ! ====================================== ! subroutine parallel_init use parallel use parser implicit none integer :: ierr integer :: size_real,size_dp ! Initialize a first basic MPI environment !##### This is where it stall out ######### call MPI_INIT(ierr) call MPI_COMM_RANK(MPI_COMM_WORLD,irank,ierr) call MPI_COMM_SIZE(MPI_COMM_WORLD,nproc,ierr) irank = irank+1 iroot = 1 ! Set MPI working precision - WP call MPI_TYPE_SIZE(MPI_REAL,size_real,ierr) call MPI_TYPE_SIZE(MPI_DOUBLE_PRECISION,size_dp,ierr) if (WP .eq. size_real) then MPI_REAL_WP = MPI_REAL else if (WP .eq. size_dp) then MPI_REAL_WP = MPI_DOUBLE_PRECISION else call parallel_kill('Error in parallel_init: no WP equivalent in MPI') end if ! Set MPI single precision call MPI_TYPE_SIZE(MPI_REAL,size_real,ierr) call MPI_TYPE_SIZE(MPI_DOUBLE_PRECISION,size_dp,ierr) if (SP .eq. size_real) then MPI_REAL_SP = MPI_REAL else if (SP .eq. size_dp) then MPI_REAL_SP = MPI_DOUBLE_PRECISION else call parallel_kill('Error in parallel_init: no SP equivalent in MPI') end if ! For now, comm should point to MPI_COMM_WORLD comm = MPI_COMM_WORLD return end subroutine parallel_init ! ============================= !

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Re: [mpich-discuss] SOS!!
by Darius Buntinas 06 Dec '12

06 Dec '12

After you add it to your .bash_profile, you'll need to log out and log back in again. Or, you could just type PATH=/Users/delfinagarciapintos/mpich2-install/bin:$PATH in the terminal to set the path manually. -d On Dec 5, 2012, at 10:23 PM, Delfina García Pintos wrote: > Dear Darius, > > Thank you so much for your answer!!! > > I did "make install" and I'm attaching mi.txt. > Also in my .bash_profile I added: > PATH=/Users/delfinagarciapintos/mpich2-install/bin:$PATH > export PATH > > I keep on trying, but nothing happens... > > Thank you :) ! > > Delfina > > > > > > Date: Wed, 5 Dec 2012 07:10:13 -0800 > > > > Did you do a "make install"? Also make sure that /Users/delfinagarciapintos/mpich2-install/bin is in your path. > > > > -d > > > > > > On Dec 4, 2012, at 9:33 PM, Delfina García Pintos wrote: > > > > > I'm trying to install MPICH2 on my MacOS 10.6. I have problems with mpif90. But not just that: when I write on the console "which mpi(run/exec/f77/f90/..)" the path is not displayed. > > > Thank you in advance! > > > > > > Delfina > > > > > > > > > > > > <c.txt><m.txt> > > > <mi.txt>

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Re: [mpich-discuss] SOS!!
by Delfina García Pintos 05 Dec '12

05 Dec '12

Dear Darius, Thank you so much for your answer!!! I did "make install" and I'm attaching mi.txt. Also in my .bash_profile I added:PATH=/Users/delfinagarciapintos/mpich2-install/bin:$PATHexport PATH I keep on trying, but nothing happens... Thank you :) ! Delfina > Date: Wed, 5 Dec 2012 07:10:13 -0800 > > Did you do a "make install"? Also make sure that /Users/delfinagarciapintos/mpich2-install/bin is in your path. > > -d > > > On Dec 4, 2012, at 9:33 PM, Delfina García Pintos wrote: > > > I'm trying to install MPICH2 on my MacOS 10.6. I have problems with mpif90. But not just that: when I write on the console "which mpi(run/exec/f77/f90/..)" the path is not displayed. > > Thank you in advance! > > > > Delfina > > > > > > > > <c.txt><m.txt> >

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Re: [mpich-discuss] Error in c.txt nemesis does not exist
by Ayesha Ghani 05 Dec '12

05 Dec '12

Hi Dave Thanks for your help! I have tried to install a few versions of MPICH2 on cygwin now. For version 2-1.4, the c.txt file seems fine (no errors) but the m.txt file goes on for a while 'Entering directory' and 'Leaving directory' and then at the end outputs an error. make[1]: *** No rule to make target '/home/agha023/libraries/mpich2-1.4/src/mpl/Makefile.am' needed by '/home/agha023/libraries/mpich2-1.4/src/mpl/Makefile.in'. Stop make: *** [all-redirect] Error 1 >From searching up forums this error occurs because make couldnt find instructions in the Makefile.in to build the target. However Makefile.am and Makefile.in both exist in the directory above. Again however I can't find a solution to this problem and would greatly appreciate any help. Should I email the m.txt and c.txt files? Kind Regards Ayesha Ghani On 6 December 2012 08:03, Dave Goodell <goodell(a)mcs.anl.gov> wrote: > Try using mpich2-1.4 instead. It would not be surprising if there was a > problem with 1.5 on cygwin. > > -Dave > > On Dec 4, 2012, at 8:48 PM PST, Ayesha Ghani wrote: > > > Hello > > > > > > I was working through the installation instructions for mpich2 very > carefully this time and my .c file has an error at the end: > > 'immediate ERROR: nemesis does not exist' > > > > I would appreciate any assistance. > > > > > > Kind Regards > > Ayesha > > <c.txt>_______________________________________________ > > discuss mailing list discuss(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss >

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Re: [mpich-discuss] Error in c.txt nemesis does not exist
by Dave Goodell 05 Dec '12

05 Dec '12

Try using mpich2-1.4 instead. It would not be surprising if there was a problem with 1.5 on cygwin. -Dave On Dec 4, 2012, at 8:48 PM PST, Ayesha Ghani wrote: > Hello > > > I was working through the installation instructions for mpich2 very carefully this time and my .c file has an error at the end: > 'immediate ERROR: nemesis does not exist' > > I would appreciate any assistance. > > > Kind Regards > Ayesha > <c.txt>_______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] Installation problems MPICH2 on cygwin
by Dave Goodell 05 Dec '12

05 Dec '12

If your "c.txt" was empty then you probably didn't successfully run configure. Since you didn't run configure successfully, no makefiles were generated, causing the error message in your m.txt file. -Dave On Dec 4, 2012, at 6:09 PM PST, Ayesha Ghani wrote: > Hi > > I was following the MPICH2 installation guide ad got up to step 6 alright. The c.txt file was empty after step 5 but I got an error in the .m file following step 6, 'Build MPICH2' > > Do you have an idea of what is wrong or how i can fix the problem? > > > Kind Regards > Ayesha Ghani > > > <m.txt>_______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

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Error in c.txt nemesis does not exist
by Ayesha Ghani 04 Dec '12

04 Dec '12

Hello I was working through the installation instructions for mpich2 very carefully this time and my .c file has an error at the end: 'immediate ERROR: nemesis does not exist' I would appreciate any assistance. Kind Regards Ayesha

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Fwd: Installation problems MPICH2 on cygwin
by Ayesha Ghani 04 Dec '12

04 Dec '12

Hi I was following the MPICH2 installation guide ad got up to step 6 alright. The c.txt file was empty after step 5 but I got an error in the .m file following step 6, 'Build MPICH2' Do you have an idea of what is wrong or how i can fix the problem? Kind Regards Ayesha Ghani

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Re: [mpich-discuss] Why does MPI_Init() get NULL argc and argv when running Fortran programs?
by clara 04 Dec '12

04 Dec '12

Thanks a lot. On Tue, Dec 4, 2012 at 3:36 AM, Jeff Hammond <jhammond(a)alcf.anl.gov> wrote: > As far as I can tell, there's no standard way to access argc/argv from > Fortran until Fortran 2003 > (http://fortranwiki.org/fortran/show/Command-line+arguments) Until > MPI-3, the Fortran bindings were targeting FORTRAN 77 and Fortran 90 > and 95 (and somewhat awkwardly), so there was no reasonable way to try > to deal with them. > > Now that there are Fortran 2008 bindings in MPI-3, it might be > interesting to consider how to handle argc/argv in a nice way just as > is done for C. I don't know if anyone has thought of what happens > when Fortran 2003+ users use the argc/argv access routines. It would > seem that the same problem would exist that is present if one accesses > argc/argv in C before MPI_INIT is called (i.e. argc/argv will have > mpiexec-related arguments, not just the ones relative to the user > program). > > I created a ticket with the MPI Forum about this: > https://svn.mpi-forum.org/trac/mpi-forum-web/ticket/351. > > Best, > > Jeff > > On Mon, Dec 3, 2012 at 9:19 AM, Rajeev Thakur <thakur(a)mcs.anl.gov> wrote: > > The Fortran binding for MPI_Init is > > > > MPI_INIT(IERROR) > > > > There are no command line arguments. > > > > Rajeev > > > > > > On Dec 3, 2012, at 6:22 AM, clara wrote: > > > >> Hi, > >> > >> I added a print statement at the beginning of MPI_Init() in mpich2-1.4 > in order to check the arguments of MPI_Init(). When running a Fortran > program, e.g. ep.S.1, the arguments of MPI_Init() are NULL; however, when > running a C program, e.g. is.S.1, *argc of MPI_Init() is 1 and (*argv)[0] > points to the name of the executed file is.S.1. > >> Can anyone tell us why there is difference in dealing with arguments of > MPI_Init() between C and Fortran programs? How could arguments be > transferred to MPI_Init() for Fortran programs in mpich2? Thanks. > >> > >> Best, > >> Clara > >> _______________________________________________ > >> discuss mailing list discuss(a)mpich.org > >> To manage subscription options or unsubscribe: > >> https://lists.mpich.org/mailman/listinfo/discuss > > > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > -- > Jeff Hammond > Argonne Leadership Computing Facility > University of Chicago Computation Institute > jhammond(a)alcf.anl.gov / (630) 252-5381 > http://www.linkedin.com/in/jeffhammond > https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss >

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Re: [mpich-discuss] Why does MPI_Init() get NULL argc and argv when running Fortran programs?
by Jeff Hammond 03 Dec '12

03 Dec '12

As far as I can tell, there's no standard way to access argc/argv from Fortran until Fortran 2003 (http://fortranwiki.org/fortran/show/Command-line+arguments) Until MPI-3, the Fortran bindings were targeting FORTRAN 77 and Fortran 90 and 95 (and somewhat awkwardly), so there was no reasonable way to try to deal with them. Now that there are Fortran 2008 bindings in MPI-3, it might be interesting to consider how to handle argc/argv in a nice way just as is done for C. I don't know if anyone has thought of what happens when Fortran 2003+ users use the argc/argv access routines. It would seem that the same problem would exist that is present if one accesses argc/argv in C before MPI_INIT is called (i.e. argc/argv will have mpiexec-related arguments, not just the ones relative to the user program). I created a ticket with the MPI Forum about this: https://svn.mpi-forum.org/trac/mpi-forum-web/ticket/351. Best, Jeff On Mon, Dec 3, 2012 at 9:19 AM, Rajeev Thakur <thakur(a)mcs.anl.gov> wrote: > The Fortran binding for MPI_Init is > > MPI_INIT(IERROR) > > There are no command line arguments. > > Rajeev > > > On Dec 3, 2012, at 6:22 AM, clara wrote: > >> Hi, >> >> I added a print statement at the beginning of MPI_Init() in mpich2-1.4 in order to check the arguments of MPI_Init(). When running a Fortran program, e.g. ep.S.1, the arguments of MPI_Init() are NULL; however, when running a C program, e.g. is.S.1, *argc of MPI_Init() is 1 and (*argv)[0] points to the name of the executed file is.S.1. >> Can anyone tell us why there is difference in dealing with arguments of MPI_Init() between C and Fortran programs? How could arguments be transferred to MPI_Init() for Fortran programs in mpich2? Thanks. >> >> Best, >> Clara >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- Jeff Hammond Argonne Leadership Computing Facility University of Chicago Computation Institute jhammond(a)alcf.anl.gov / (630) 252-5381 http://www.linkedin.com/in/jeffhammond https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond

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