November 2013 - discuss - mailman3.cels.anl.gov

double free error after MPI run finished
by John Bray 08 Nov '13

08 Nov '13

I've got some sample code that I'm using to test our debugger DDT. It works on openmpi and intelmpi, but with all the MPICH series from MPICH2 onwards to 3.1rc1, I get an error after MPI_FINALIZE. Our memory debugging library claims its at SendqFreePool (dbginit.c:386) trying to free previously freed pointer with a stacktrrace auditmpi pmpi_finalize__ PMPI__finalize MPIR_Call_finalize_callbacks sendqFreePool (dbginit.c) Run from a raw mpirun command outside DDT *** glibc detected *** ./auditmpibad_f_debug.exe: double free or corruption (fasttop): 0x1032a5c8 *** *** glibc detected *** ./auditmpibad_f_debug.exe: double free or corruption (fasttop): 0x104da5c8 *** ======= Backtrace: ========= ======= Backtrace: ========= /lib/libc.so.6(+0xfe750e4)[0xf78e50e4] /home/jbray/prog/mpich/mpich-3.1rc1/rhel-6-ppc64_ibm/install/lib/libmpich.so.11(+0x1a8b1c)[0xfec8b1c] /lib/libc.so.6(+0xfe750e4)[0xf76c50e4] /home/jbray/prog/mpich/mpich-3.1rc1/rhel-6-ppc64_ibm/install/lib/libmpich.so.11(+0x1a8b1c)[0xfec8b1c] ... and so on I've configured with ./configure --prefix=$PWD/install --enable-shared --enable-fast=all --enable-debuginfo and compile with mpif90 -o auditmpibad_f_debug.exe auditmpibad.F90 -O0 -g Its works with the ALLTOALLV only called once. Is this a bug or a misunderstanding on my part. The code is program auditmpi use mpi, only : & MPI_COMM_WORLD, & MPI_REAL, & MPI_STATUS_SIZE, & MPI_BSEND_OVERHEAD, & MPI_SUM, & MPI_UNDEFINED implicit none integer, parameter :: repeats=2 integer :: rank, nproc,ierr,rpt real :: input(100000),output(100000) integer :: status (MPI_STATUS_SIZE) integer :: statuses (MPI_STATUS_SIZE,repeats) integer :: request logical :: odd integer, allocatable :: recvcounts(:),sendcounts(:),displs(:) call MPI_INIT(ierr) call MPI_COMM_RANK(MPI_COMM_WORLD, rank, ierr) call MPI_COMM_SIZE(MPI_COMM_WORLD, nproc, ierr) if (rank == 0) print *,"auditmpi start" if (mod(rank,2) == 0) then odd=.false. else odd=.true. end if allocate (recvcounts(nproc)) recvcounts(:) = 100000/nproc allocate (sendcounts(nproc)) sendcounts(:) = 100000/nproc allocate (displs(nproc)) displs(:)=0 ! don't care if we overlap if ( .NOT. odd) then call MPI_IRECV(output,size(output),MPI_REAL,rank+1,1,MPI_COMM_WORLD, request, ierr) end if call MPI_BARRIER(MPI_COMM_WORLD,ierr) if (odd) then call MPI_IRSEND(input,size(input),MPI_REAL,rank-1,1,MPI_COMM_WORLD,request,ierr) end if call MPI_WAIT(request,status,ierr) do rpt=1,2 call MPI_ALLTOALLV(input,sendcounts,displs,MPI_REAL,output,recvcounts,displs,MPI_REAL,MPI_COMM_WORLD,ierr) end do call MPI_BARRIER(MPI_COMM_WORLD,ierr) deallocate (recvcounts) deallocate (sendcounts) deallocate (displs) if (rank == 0) print *,"auditmpi finished" call MPI_FINALIZE(ierr) end program auditmpi John

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Re: [mpich-discuss] Error when building MPI with --enbale-shared
by Antonio J. Peña 08 Nov '13

08 Nov '13

A quick test I may suggest is trying our latest release (rc1). --enable- shared is the default, and we fixed a few things there. Antonio On Friday, November 08, 2013 06:26:09 PM Lokman Rahmani wrote: Hello, When building MPICH3 with the option --enable-shared the build fails with the error : /usr/bin/ld: /home/hpc/build/mpich-3.0.4/src/mpl/.libs/libmpl.a(mpltrmem.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with - fPIC/home/hpc/build/mpich-3.0.4/src/mpl/.libs/libmpl.a: could not read symbols: Bad value About this error message, I found this (old) discussion in the mailing list archive : https://lists.mcs.anl.gov/mailman/htdig/mpich-discuss/2011-January/008727.h… What i understood from this message is that I have to use --disable-rpath (wich become --disable-wrapper-rpath for the newer versions), but i still have the same problem.(I also set the CXXFLAGS and CFLAGS to -fPIC) Anyone can give me hints about the reasons of this error and how to overcome it? Thank youLokman

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Error when building MPI with --enbale-shared
by Lokman Rahmani 08 Nov '13

08 Nov '13

Hello, When building MPICH3 with the option --enable-shared the build fails with the error : /usr/bin/ld: /home/hpc/build/mpich-3.0.4/src/mpl/.libs/libmpl.a(mpltrmem.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC /home/hpc/build/mpich-3.0.4/src/mpl/.libs/libmpl.a: could not read symbols: Bad value About this error message, I found this (old) discussion in the mailing list archive : https://lists.mcs.anl.gov/mailman/htdig/mpich-discuss/2011-January/008727.h… What i understood from this message is that I have to use --disable-rpath (wich become --disable-wrapper-rpath for the newer versions), but i still have the same problem . (I also set the CXXFLAGS and CFLAGS to -fPIC) Anyone can give me hints about the reasons of this error and how to overcome it? Thank you Lokman

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Re: [mpich-discuss] MPICH2 - smpd passphrase
by Wesley Bland 08 Nov '13

08 Nov '13

As predicted: Unfortunately, we haven't supported Windows since MPICH version 1.4.1p1. You can find out more at the FAQ page: http://wiki.mpich.org/mpich/index.php/Frequently_Asked_Questions#Q:_Why_can… You can try the information there or you can try your question on some other places (Stack Overflow for example). I don’t know anything about Windows, but a quick glance at your question suggests that you don’t have passwordless SSH set up correctly. You might try taking a look at that. Thanks, Wesley On Nov 8, 2013, at 6:37 AM, Jonathan Kaufman <j14kaufman(a)gmail.com> wrote: > I know there isn't much support for MPICH2 on windows, but here goes. I am trying to run MPICH2 on a 64 bit windows 8. (I have mpiexec, smpd, and input files in the same directory) > I did the following under cmd as an admin: > smpd -install > mpiexec -remove > mpiexec - register (used username and password) > mpiexec -validate ( success) > smpd -status (it says it is running) > mpiexec.exe -np 4 -localonly lmp_win_mpi < in.crack > This last line asks me for the passphrase, however the correct passphrase does not work, and I have to abort out of the screen. > > Any help would be greatly appreciated. > > Sincerely, > Jonathan > > -- > Jonathan Kaufman > Materials Science & Engineering, Drexel University > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

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MPICH2 - smpd passphrase
by Jonathan Kaufman 08 Nov '13

08 Nov '13

I know there isn't much support for MPICH2 on windows, but here goes. I am trying to run MPICH2 on a 64 bit windows 8. (I have mpiexec, smpd, and input files in the same directory) I did the following under cmd as an admin: smpd -install mpiexec -remove mpiexec - register (used username and password) mpiexec -validate ( success) smpd -status (it says it is running) mpiexec.exe -np 4 -localonly lmp_win_mpi < in.crack This last line asks me for the passphrase, however the correct passphrase does not work, and I have to abort out of the screen. Any help would be greatly appreciated. Sincerely, Jonathan -- Jonathan Kaufman Materials Science & Engineering, Drexel University

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Re: [mpich-discuss] Compilation: MPICH3 and libxml2
by Mogesh Naidoo 08 Nov '13

08 Nov '13

Hi Junchao, Many thanks! The compile is now successful. I still have to test with WRF now. regards, Mogesh. >>> Junchao Zhang <jczhang(a)mcs.anl.gov> 06/11/2013 17:26 >>> It seems the compilation was stuck at hwloc. Try export these two env variables and compile again. HWLOC_LIBXML2_CFLAGS = -I<path to your xml2 headers, such as /usr/include/libxml2> HWLOC_LIBXML2_LIBS = -L<path to your xml2 library> -lxml2 If it does not work, could you paste your $LD_LIBRARY_PATH? --Junchao Zhang On Tue, Nov 5, 2013 at 6:52 AM, Mogesh Naidoo <MNaidoo4(a)csir.co.za> wrote: Hi, I'm having trouble compiling MPICH-3.0.4. I'm using GNU 4.7.2 compilers. My configure = ./configure --prefix=/export/home/mnaidoo/software/mpich/mpich3_GNU --with-gnu-ld 2>&1 | tee c.txt Configure is successful with no errors. The make fails with "libtool: link: `/usr/lib64/libxml2.la' is not a valid libtool archive" This occurs when trying: "CCLD libhwloc_embedded.la" So there's a libxml2.la in /usr/lib64, but there's also one in another directory. I add this directory to LD_LIBRARY_PATH and I still get the same error. How do I tell make to use the libxml2.la in the other directory? regards, Mogesh. -- This message is subject to the CSIR's copyright terms and conditions, e-mail legal notice, and implemented Open Document Format (ODF) standard. The full disclaimer details can be found at http://www.csir.co.za/disclaimer.html. This message has been scanned for viruses and dangerous content by MailScanner ( http://www.mailscanner.info/) , and is believed to be clean. Please consider the environment before printing this email. _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss -- This message is subject to the CSIR's copyright terms and conditions, e-mail legal notice, and implemented Open Document Format (ODF) standard. The full disclaimer details can be found at http://www.csir.co.za/disclaimer.html. This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. Please consider the environment before printing this email.

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Re: [mpich-discuss] MPICH 3.1rc1 packages for Ubuntu, Debian and Slackware (x86 and amd64)
by Antonio J. Peña 07 Nov '13

07 Nov '13

Thanks Marcelo. I'll post them in our website. Antonio On Thursday, November 07, 2013 01:44:35 PM Marcelo Soares Souza wrote: > mpich-3.1rc1 packages > > * Ubuntu 13.04 (Saucy Salamander) > > - amd64 > http://www.cebacad.net/files/mpich/ubuntu/mpich-3.1rc1/mpich_3.1rc1-1ubuntu_ > amd64.deb > > - x86 > http://www.cebacad.net/files/mpich/ubuntu/mpich-3.1rc1/mpich_3.1rc1-1ubuntu_ > i386.deb > > * Debian 7.2.0 (Wheezy) > > - amd64 > http://www.cebacad.net/files/mpich/debian/mpich-3.1rc1/mpich_3.1rc1-1debian_ > amd64.deb > > - x86 > http://www.cebacad.net/files/mpich/debian/mpich-3.1rc1/mpich_3.1rc1-1debian_ > i386.deb > > * Slackware 14.1 > > - amd64 > http://www.cebacad.net/files/mpich/slackware/mpich-3.1rc1/mpich-3.1rc1-x86_6 > 4-goa-1.txz > > - x86 > http://www.cebacad.net/files/mpich/slackware/mpich-3.1rc1/mpich-3.1rc1-i486-> goa-1.txz > > Enjoy! ;)

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MPICH 3.1rc1 packages for Ubuntu, Debian and Slackware (x86 and amd64)
by Marcelo Soares Souza 07 Nov '13

07 Nov '13

mpich-3.1rc1 packages * Ubuntu 13.04 (Saucy Salamander) - amd64 http://www.cebacad.net/files/mpich/ubuntu/mpich-3.1rc1/mpich_3.1rc1-1ubuntu… - x86 http://www.cebacad.net/files/mpich/ubuntu/mpich-3.1rc1/mpich_3.1rc1-1ubuntu… * Debian 7.2.0 (Wheezy) - amd64 http://www.cebacad.net/files/mpich/debian/mpich-3.1rc1/mpich_3.1rc1-1debian… - x86 http://www.cebacad.net/files/mpich/debian/mpich-3.1rc1/mpich_3.1rc1-1debian… * Slackware 14.1 - amd64 http://www.cebacad.net/files/mpich/slackware/mpich-3.1rc1/mpich-3.1rc1-x86_… - x86 http://www.cebacad.net/files/mpich/slackware/mpich-3.1rc1/mpich-3.1rc1-i486… Enjoy! ;) -- Marcelo Soares Souza https://marcelo.juntadados.org Diaspora* https://diaspora.juntadados.org/u/marcelo Friendica http://friendica.ambientedigital.org/profile/marcelo

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Re: [mpich-discuss] MPICH error on CentOS
by Ricardo Román Brenes 06 Nov '13

06 Nov '13

yup. On Wed, Nov 6, 2013 at 9:25 PM, bharat gupta <bharat.85.monu(a)gmail.com>wrote: > Okay .. thanks but right now my simulation is running and if I use the > command that you both mentioned would ultimately lead to the stoppage of my > simulations .. right ?? May be I can try reinstalling the new version after > finishing the simulations > > > On Thu, Nov 7, 2013 at 12:21 PM, Ricardo Román Brenes < > roman.ricardo(a)gmail.com> wrote: > >> both will coexiste, you ahve to "yum remove mpich2-x-x-x.x84_64" >> >> >> On Wed, Nov 6, 2013 at 9:20 PM, bharat gupta <bharat.85.monu(a)gmail.com>wrote: >> >>> But how to remove the older version or reinstalling the new one will >>> override the changes >>> >>> >>> On Thu, Nov 7, 2013 at 12:18 PM, Pavan Balaji <balaji(a)mcs.anl.gov>wrote: >>> >>>> >>>> Wow. 1.2.1p1 is ancient. It was used by dinosaurs and such when they >>>> still roamed the earth. >>>> >>>> I don’t use CentOS, but don’t the rpm’s from this page work? >>>> >>>> http://www.mpich.org/downloads/ >>>> >>>> If not, then source compile is always possible. :-) It’s an >>>> open-source project. >>>> >>>> —- Pavan >>>> >>>> On Nov 6, 2013, at 6:56 PM, bharat gupta <bharat.85.monu(a)gmail.com> >>>> wrote: >>>> >>>> > Okay.. Thanks a lot for your time and help.. >>>> > >>>> > >>>> > On Thu, Nov 7, 2013 at 9:54 AM, Ricardo Román Brenes < >>>> roman.ricardo(a)gmail.com> wrote: >>>> > You have to either remove the old rpm and compile a new version or >>>> remove the old version and create an rpm from the source. Maybe fedora or >>>> suse have a newer version in their repos but I havent checked >>>> > >>>> > On Nov 6, 2013 6:48 PM, "bharat gupta" <bharat.85.monu(a)gmail.com> >>>> wrote: >>>> > How can that be done in CentOS 6.0, I used the command yum search >>>> mpich and installed the one that it showed ... >>>> > >>>> > >>>> > On Thu, Nov 7, 2013 at 9:47 AM, Ricardo Román Brenes < >>>> roman.ricardo(a)gmail.com> wrote: >>>> > Still, try to update to a new mpich asap! :-) >>>> > >>>> > On Nov 6, 2013 6:45 PM, "bharat gupta" <bharat.85.monu(a)gmail.com> >>>> wrote: >>>> > Thanks for the command. After issuing mpdboot and making file >>>> mdp.conf with line secretword=<> in /etc folder solved the problem.. >>>> > >>>> > Thanks a lot >>>> > >>>> > >>>> > On Thu, Nov 7, 2013 at 9:43 AM, bharat gupta < >>>> bharat.85.monu(a)gmail.com> wrote: >>>> > I didn't use any of these command , I issued the command 'mpirun -np >>>> 24 mdrun -v -deffnm mdrun' for running the gromacs' and after using this >>>> command I got those errors >>>> > >>>> > >>>> > On Thu, Nov 7, 2013 at 9:42 AM, Ricardo Román Brenes < >>>> roman.ricardo(a)gmail.com> wrote: >>>> > Did you start mpd either with mpd or mpdboot? >>>> > >>>> > On Nov 6, 2013 6:39 PM, "Ricardo Román Brenes" < >>>> roman.ricardo(a)gmail.com> wrote: >>>> > He has to. Thats an older mpich than mine! :-P >>>> > >>>> > On Nov 6, 2013 6:34 PM, "Pavan Balaji" <balaji(a)mcs.anl.gov> wrote: >>>> > >>>> > Looks like I’m late to this email chain. >>>> > >>>> > Please don’t use mpd. mpd has been deprecated for many releases of >>>> mpich now. You might be using a very old version of mpich. >>>> > >>>> > —- Pavan >>>> > >>>> > On Nov 6, 2013, at 6:26 PM, bharat gupta <bharat.85.monu(a)gmail.com> >>>> wrote: >>>> > >>>> > > DO I need to add some command in mpd.hosts file >>>> > > >>>> > > >>>> > > On Thu, Nov 7, 2013 at 9:22 AM, bharat gupta < >>>> bharat.85.monu(a)gmail.com> wrote: >>>> > > I don't know much about mpi , as I am using gromacs which was >>>> complied with mpi option. , But I read somewhere that >>>> > > >>>> > > " If a file named .mpd.conf is available in the user's home >>>> directory, only the user can have read and write privileges. The file must >>>> minimally contain a line with secretword=<secretword>. If you want to run >>>> MPD as root, create the mpd.conf file in the /etc directory instead of >>>> .mpd.conf in the root's home directory to run mpd as root. Avoid starting >>>> the MPD ring under the root account." Here'e the link >>>> http://software.intel.com/sites/products/documentation/hpc/ics/impi/41/lin/… >>>> > > >>>> > > And after using chmod 700 , I still get the same error, but when I >>>> create a file mpd.conf in /etc I get the and added the >>>> secretword=<secretword> line in the file and run the same command, I get >>>> this error:- >>>> > > >>>> > > root@localhost INGT]# mpirun -np 24 mdrun -v -deffnm mdrun >>>> > > mpdroot: perror msg: No such file or directory >>>> > > mpdroot: cannot connect to local mpd at: /tmp/mpd2.console_root >>>> > > probable cause: no mpd daemon on this machine >>>> > > possible cause: unix socket /tmp/mpd2.console_root has been >>>> removed >>>> > > >>>> > > mpiexec_localhost.localdomain (__init__ 1208): forked process >>>> failed; status=255 >>>> > > >>>> > > >>>> > > On Thu, Nov 7, 2013 at 9:11 AM, Ricardo Román Brenes < >>>> roman.ricardo(a)gmail.com> wrote: >>>> > > Try using chmod 700. Can you run any other mpi example? Like cpi.c >>>> > > >>>> > > On Nov 6, 2013 6:08 PM, "bharat gupta" <bharat.85.monu(a)gmail.com> >>>> wrote: >>>> > > It have changed the file permission (rw) for root , ls -l mpd.hosts >>>> gives the output >>>> > > -rw-r--r--, 1 root root >>>> > > >>>> > > >>>> > > On Thu, Nov 7, 2013 at 9:02 AM, Ricardo Román Brenes < >>>> roman.ricardo(a)gmail.com> wrote: >>>> > > With rwx permission just for root? >>>> > > >>>> > > On Nov 6, 2013 6:00 PM, "bharat gupta" <bharat.85.monu(a)gmail.com> >>>> wrote: >>>> > > I have created the file mpd.hosts in /etc folder in the root , but >>>> still it shows the same error ... /usr/bin/mpdroot: open failed for root's >>>> mpd conf filempiexec_localhost.localdomain (__init__ 1208): forked process >>>> failed; status=255 >>>> > > >>>> > > >>>> > > On Thu, Nov 7, 2013 at 8:45 AM, Ricardo Román Brenes < >>>> roman.ricardo(a)gmail.com> wrote: >>>> > > You need to create a mpd.hosts in /etc if you want to run mpd as >>>> root >>>> > > >>>> > > On Nov 6, 2013 5:41 PM, "bharat gupta" <bharat.85.monu(a)gmail.com> >>>> wrote: >>>> > > Hi, >>>> > > >>>> > > I am getting the following error while using the command - >>>> > > >>>> > > [root@localhost INGT]# mpirun -np 24 mdrun_mpi -v -deffnm npt >>>> > > >>>> > > Error - >>>> > > >>>> > > /usr/bin/mpdroot: open failed for root's mpd conf >>>> filempiexec_localhost.localdomain (__init__ 1208): forked process failed; >>>> status=255 >>>> > > >>>> > > I complied gromacs using - ./configure --enable-shared >>>> --enable-mpi. I have installed the mpich package , this is what I get when >>>> I check for mpirun and mpiexec - >>>> > > >>>> > > [root@localhost /]# which mpirun >>>> > > /usr/bin/mpirun >>>> > > [root@localhost /]# which mpiexec >>>> > > /usr/bin/mpiexec >>>> > > >>>> > > What could be the problem here ?? >>>> > > >>>> > > Thanks >>>> > > -------- >>>> > > Bharat >>>> > > >>>> > > >>>> > > >>>> > > _______________________________________________ >>>> > > 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 >>>> > > >>>> > > >>>> > > >>>> > > -- >>>> > > Bharat >>>> > > Ph.D. Candidate >>>> > > Biomolecular Engineering Laboratory >>>> > > Pusan National University >>>> > > South Korea >>>> > > Mobile no. - 010-5818-3680 >>>> > > >>>> > > >>>> > > _______________________________________________ >>>> > > 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 >>>> > > >>>> > > >>>> > > >>>> > > -- >>>> > > Bharat >>>> > > Ph.D. Candidate >>>> > > Biomolecular Engineering Laboratory >>>> > > Pusan National University >>>> > > South Korea >>>> > > Mobile no. - 010-5818-3680 >>>> > > >>>> > > >>>> > > _______________________________________________ >>>> > > 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 >>>> > > >>>> > > >>>> > > >>>> > > -- >>>> > > Bharat >>>> > > Ph.D. Candidate >>>> > > Biomolecular Engineering Laboratory >>>> > > Pusan National University >>>> > > South Korea >>>> > > Mobile no. - 010-5818-3680 >>>> > > >>>> > > >>>> > > >>>> > > >>>> > > -- >>>> > > Bharat >>>> > > Ph.D. Candidate >>>> > > Biomolecular Engineering Laboratory >>>> > > Pusan National University >>>> > > South Korea >>>> > > Mobile no. - 010-5818-3680 >>>> > > >>>> > > _______________________________________________ >>>> > > discuss mailing list discuss(a)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(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 >>>> > >>>> > >>>> > >>>> > -- >>>> > Bharat >>>> > Ph.D. Candidate >>>> > Biomolecular Engineering Laboratory >>>> > Pusan National University >>>> > South Korea >>>> > Mobile no. - 010-5818-3680 >>>> > >>>> > >>>> > >>>> > >>>> > -- >>>> > Bharat >>>> > Ph.D. Candidate >>>> > Biomolecular Engineering Laboratory >>>> > Pusan National University >>>> > South Korea >>>> > Mobile no. - 010-5818-3680 >>>> > >>>> > >>>> > _______________________________________________ >>>> > 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 >>>> > >>>> > >>>> > >>>> > -- >>>> > Bharat >>>> > Ph.D. Candidate >>>> > Biomolecular Engineering Laboratory >>>> > Pusan National University >>>> > South Korea >>>> > Mobile no. - 010-5818-3680 >>>> > >>>> > >>>> > _______________________________________________ >>>> > 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 >>>> > >>>> > >>>> > >>>> > -- >>>> > Bharat >>>> > Ph.D. Candidate >>>> > Biomolecular Engineering Laboratory >>>> > Pusan National University >>>> > South Korea >>>> > Mobile no. - 010-5818-3680 >>>> > >>>> > _______________________________________________ >>>> > discuss mailing list discuss(a)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(a)mpich.org >>>> To manage subscription options or unsubscribe: >>>> https://lists.mpich.org/mailman/listinfo/discuss >>>> >>> >>> >>> >>> -- >>> Bharat >>> Ph.D. Candidate >>> Biomolecular Engineering Laboratory >>> Pusan National University >>> South Korea >>> Mobile no. - 010-5818-3680 >>> >>> >>> _______________________________________________ >>> 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 >> > > > > -- > Bharat > Ph.D. Candidate > Biomolecular Engineering Laboratory > Pusan National University > South Korea > Mobile no. - 010-5818-3680 > > > _______________________________________________ > 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] MPICH error on CentOS
by bharat gupta 06 Nov '13

06 Nov '13

Okay .. thanks but right now my simulation is running and if I use the command that you both mentioned would ultimately lead to the stoppage of my simulations .. right ?? May be I can try reinstalling the new version after finishing the simulations On Thu, Nov 7, 2013 at 12:21 PM, Ricardo Román Brenes < roman.ricardo(a)gmail.com> wrote: > both will coexiste, you ahve to "yum remove mpich2-x-x-x.x84_64" > > > On Wed, Nov 6, 2013 at 9:20 PM, bharat gupta <bharat.85.monu(a)gmail.com>wrote: > >> But how to remove the older version or reinstalling the new one will >> override the changes >> >> >> On Thu, Nov 7, 2013 at 12:18 PM, Pavan Balaji <balaji(a)mcs.anl.gov> wrote: >> >>> >>> Wow. 1.2.1p1 is ancient. It was used by dinosaurs and such when they >>> still roamed the earth. >>> >>> I don’t use CentOS, but don’t the rpm’s from this page work? >>> >>> http://www.mpich.org/downloads/ >>> >>> If not, then source compile is always possible. :-) It’s an >>> open-source project. >>> >>> —- Pavan >>> >>> On Nov 6, 2013, at 6:56 PM, bharat gupta <bharat.85.monu(a)gmail.com> >>> wrote: >>> >>> > Okay.. Thanks a lot for your time and help.. >>> > >>> > >>> > On Thu, Nov 7, 2013 at 9:54 AM, Ricardo Román Brenes < >>> roman.ricardo(a)gmail.com> wrote: >>> > You have to either remove the old rpm and compile a new version or >>> remove the old version and create an rpm from the source. Maybe fedora or >>> suse have a newer version in their repos but I havent checked >>> > >>> > On Nov 6, 2013 6:48 PM, "bharat gupta" <bharat.85.monu(a)gmail.com> >>> wrote: >>> > How can that be done in CentOS 6.0, I used the command yum search >>> mpich and installed the one that it showed ... >>> > >>> > >>> > On Thu, Nov 7, 2013 at 9:47 AM, Ricardo Román Brenes < >>> roman.ricardo(a)gmail.com> wrote: >>> > Still, try to update to a new mpich asap! :-) >>> > >>> > On Nov 6, 2013 6:45 PM, "bharat gupta" <bharat.85.monu(a)gmail.com> >>> wrote: >>> > Thanks for the command. After issuing mpdboot and making file mdp.conf >>> with line secretword=<> in /etc folder solved the problem.. >>> > >>> > Thanks a lot >>> > >>> > >>> > On Thu, Nov 7, 2013 at 9:43 AM, bharat gupta <bharat.85.monu(a)gmail.com> >>> wrote: >>> > I didn't use any of these command , I issued the command 'mpirun -np >>> 24 mdrun -v -deffnm mdrun' for running the gromacs' and after using this >>> command I got those errors >>> > >>> > >>> > On Thu, Nov 7, 2013 at 9:42 AM, Ricardo Román Brenes < >>> roman.ricardo(a)gmail.com> wrote: >>> > Did you start mpd either with mpd or mpdboot? >>> > >>> > On Nov 6, 2013 6:39 PM, "Ricardo Román Brenes" < >>> roman.ricardo(a)gmail.com> wrote: >>> > He has to. Thats an older mpich than mine! :-P >>> > >>> > On Nov 6, 2013 6:34 PM, "Pavan Balaji" <balaji(a)mcs.anl.gov> wrote: >>> > >>> > Looks like I’m late to this email chain. >>> > >>> > Please don’t use mpd. mpd has been deprecated for many releases of >>> mpich now. You might be using a very old version of mpich. >>> > >>> > —- Pavan >>> > >>> > On Nov 6, 2013, at 6:26 PM, bharat gupta <bharat.85.monu(a)gmail.com> >>> wrote: >>> > >>> > > DO I need to add some command in mpd.hosts file >>> > > >>> > > >>> > > On Thu, Nov 7, 2013 at 9:22 AM, bharat gupta < >>> bharat.85.monu(a)gmail.com> wrote: >>> > > I don't know much about mpi , as I am using gromacs which was >>> complied with mpi option. , But I read somewhere that >>> > > >>> > > " If a file named .mpd.conf is available in the user's home >>> directory, only the user can have read and write privileges. The file must >>> minimally contain a line with secretword=<secretword>. If you want to run >>> MPD as root, create the mpd.conf file in the /etc directory instead of >>> .mpd.conf in the root's home directory to run mpd as root. Avoid starting >>> the MPD ring under the root account." Here'e the link >>> http://software.intel.com/sites/products/documentation/hpc/ics/impi/41/lin/… >>> > > >>> > > And after using chmod 700 , I still get the same error, but when I >>> create a file mpd.conf in /etc I get the and added the >>> secretword=<secretword> line in the file and run the same command, I get >>> this error:- >>> > > >>> > > root@localhost INGT]# mpirun -np 24 mdrun -v -deffnm mdrun >>> > > mpdroot: perror msg: No such file or directory >>> > > mpdroot: cannot connect to local mpd at: /tmp/mpd2.console_root >>> > > probable cause: no mpd daemon on this machine >>> > > possible cause: unix socket /tmp/mpd2.console_root has been >>> removed >>> > > >>> > > mpiexec_localhost.localdomain (__init__ 1208): forked process >>> failed; status=255 >>> > > >>> > > >>> > > On Thu, Nov 7, 2013 at 9:11 AM, Ricardo Román Brenes < >>> roman.ricardo(a)gmail.com> wrote: >>> > > Try using chmod 700. Can you run any other mpi example? Like cpi.c >>> > > >>> > > On Nov 6, 2013 6:08 PM, "bharat gupta" <bharat.85.monu(a)gmail.com> >>> wrote: >>> > > It have changed the file permission (rw) for root , ls -l mpd.hosts >>> gives the output >>> > > -rw-r--r--, 1 root root >>> > > >>> > > >>> > > On Thu, Nov 7, 2013 at 9:02 AM, Ricardo Román Brenes < >>> roman.ricardo(a)gmail.com> wrote: >>> > > With rwx permission just for root? >>> > > >>> > > On Nov 6, 2013 6:00 PM, "bharat gupta" <bharat.85.monu(a)gmail.com> >>> wrote: >>> > > I have created the file mpd.hosts in /etc folder in the root , but >>> still it shows the same error ... /usr/bin/mpdroot: open failed for root's >>> mpd conf filempiexec_localhost.localdomain (__init__ 1208): forked process >>> failed; status=255 >>> > > >>> > > >>> > > On Thu, Nov 7, 2013 at 8:45 AM, Ricardo Román Brenes < >>> roman.ricardo(a)gmail.com> wrote: >>> > > You need to create a mpd.hosts in /etc if you want to run mpd as root >>> > > >>> > > On Nov 6, 2013 5:41 PM, "bharat gupta" <bharat.85.monu(a)gmail.com> >>> wrote: >>> > > Hi, >>> > > >>> > > I am getting the following error while using the command - >>> > > >>> > > [root@localhost INGT]# mpirun -np 24 mdrun_mpi -v -deffnm npt >>> > > >>> > > Error - >>> > > >>> > > /usr/bin/mpdroot: open failed for root's mpd conf >>> filempiexec_localhost.localdomain (__init__ 1208): forked process failed; >>> status=255 >>> > > >>> > > I complied gromacs using - ./configure --enable-shared --enable-mpi. >>> I have installed the mpich package , this is what I get when I check for >>> mpirun and mpiexec - >>> > > >>> > > [root@localhost /]# which mpirun >>> > > /usr/bin/mpirun >>> > > [root@localhost /]# which mpiexec >>> > > /usr/bin/mpiexec >>> > > >>> > > What could be the problem here ?? >>> > > >>> > > Thanks >>> > > -------- >>> > > Bharat >>> > > >>> > > >>> > > >>> > > _______________________________________________ >>> > > 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 >>> > > >>> > > >>> > > >>> > > -- >>> > > Bharat >>> > > Ph.D. Candidate >>> > > Biomolecular Engineering Laboratory >>> > > Pusan National University >>> > > South Korea >>> > > Mobile no. - 010-5818-3680 >>> > > >>> > > >>> > > _______________________________________________ >>> > > 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 >>> > > >>> > > >>> > > >>> > > -- >>> > > Bharat >>> > > Ph.D. Candidate >>> > > Biomolecular Engineering Laboratory >>> > > Pusan National University >>> > > South Korea >>> > > Mobile no. - 010-5818-3680 >>> > > >>> > > >>> > > _______________________________________________ >>> > > 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 >>> > > >>> > > >>> > > >>> > > -- >>> > > Bharat >>> > > Ph.D. Candidate >>> > > Biomolecular Engineering Laboratory >>> > > Pusan National University >>> > > South Korea >>> > > Mobile no. - 010-5818-3680 >>> > > >>> > > >>> > > >>> > > >>> > > -- >>> > > Bharat >>> > > Ph.D. Candidate >>> > > Biomolecular Engineering Laboratory >>> > > Pusan National University >>> > > South Korea >>> > > Mobile no. - 010-5818-3680 >>> > > >>> > > _______________________________________________ >>> > > discuss mailing list discuss(a)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(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 >>> > >>> > >>> > >>> > -- >>> > Bharat >>> > Ph.D. Candidate >>> > Biomolecular Engineering Laboratory >>> > Pusan National University >>> > South Korea >>> > Mobile no. - 010-5818-3680 >>> > >>> > >>> > >>> > >>> > -- >>> > Bharat >>> > Ph.D. Candidate >>> > Biomolecular Engineering Laboratory >>> > Pusan National University >>> > South Korea >>> > Mobile no. - 010-5818-3680 >>> > >>> > >>> > _______________________________________________ >>> > 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 >>> > >>> > >>> > >>> > -- >>> > Bharat >>> > Ph.D. Candidate >>> > Biomolecular Engineering Laboratory >>> > Pusan National University >>> > South Korea >>> > Mobile no. - 010-5818-3680 >>> > >>> > >>> > _______________________________________________ >>> > 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 >>> > >>> > >>> > >>> > -- >>> > Bharat >>> > Ph.D. Candidate >>> > Biomolecular Engineering Laboratory >>> > Pusan National University >>> > South Korea >>> > Mobile no. - 010-5818-3680 >>> > >>> > _______________________________________________ >>> > discuss mailing list discuss(a)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(a)mpich.org >>> To manage subscription options or unsubscribe: >>> https://lists.mpich.org/mailman/listinfo/discuss >>> >> >> >> >> -- >> Bharat >> Ph.D. Candidate >> Biomolecular Engineering Laboratory >> Pusan National University >> South Korea >> Mobile no. - 010-5818-3680 >> >> >> _______________________________________________ >> 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 > -- Bharat Ph.D. Candidate Biomolecular Engineering Laboratory Pusan National University South Korea Mobile no. - 010-5818-3680

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