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

Re: [mpich-discuss] install + config on windows
by spatiogis 10 Jun '13

10 Jun '13

Hello, actually, it seems that Mpich must be compiled to work. The point is that the "Readme" file gives an explanation to compile the programs with Visual studio 2003. Anyway this last software is very difficult to make work on windows 7. Is there finally a way to compile Mpich on windows 7 with Visual Studio ? best regards, Benoit Véler > Hi, > From the log output it looks like credentials (password) for > Utilisateur was not correct. > Is Utilisateur a valid Windows user on your machine? Have you > registered the username/password correctly (Try re-registering the > username+password by typing "mpiexec -register" at the command prompt)? > > Regards, > Jayesh > > ----- Original Message ----- > From: "spatiogis" <geo(a)spatiogis.fr> > To: discuss(a)mpich.org > Sent: Friday, May 3, 2013 11:58:00 AM > Subject: Re: [mpich-discuss] install + config on windows > > Hello, > > for this command : > > # C:\Progra~1\MPICH2\bin\mpiexec -verbose -n 2 > C:\Progra~1\MPICH2\examples\cpi.exe > > result : > > ....../SMPDU_Sock_post_readv > ...../SMPDU_Sock_post_read > ..../smpd_handle_op_connect > ....sock_waiting for the next event. > ....\SMPDU_Sock_wait > ..../SMPDU_Sock_wait > ....SOCK_OP_READ event.error = 0, result = 0, context=left > ....\smpd_handle_op_read > .....\smpd_state_reading_challenge_string > ......read challenge string: '1.4.1p1 18467' > ......\smpd_verify_version > ....../smpd_verify_version > ......Verification of smpd version succeeded > ......\smpd_hash > ....../smpd_hash > ......\SMPDU_Sock_post_write > .......\SMPDU_Sock_post_writev > ......./SMPDU_Sock_post_writev > ....../SMPDU_Sock_post_write > ...../smpd_state_reading_challenge_string > ..../smpd_handle_op_read > ....sock_waiting for the next event. > ....\SMPDU_Sock_wait > ..../SMPDU_Sock_wait > ....SOCK_OP_WRITE event.error = 0, result = 0, context=left > ....\smpd_handle_op_write > .....\smpd_state_writing_challenge_response > ......wrote challenge response: 'dafd1d07c1e6e9cb5fae968403d0d933' > ......\SMPDU_Sock_post_read > .......\SMPDU_Sock_post_readv > ......./SMPDU_Sock_post_readv > ....../SMPDU_Sock_post_read > ...../smpd_state_writing_challenge_response > ..../smpd_handle_op_write > ....sock_waiting for the next event. > ....\SMPDU_Sock_wait > ..../SMPDU_Sock_wait > ....SOCK_OP_READ event.error = 0, result = 0, context=left > ....\smpd_handle_op_read > .....\smpd_state_reading_connect_result > ......read connect result: 'SUCCESS' > ......\SMPDU_Sock_post_write > .......\SMPDU_Sock_post_writev > ......./SMPDU_Sock_post_writev > ....../SMPDU_Sock_post_write > ...../smpd_state_reading_connect_result > ..../smpd_handle_op_read > ....sock_waiting for the next event. > ....\SMPDU_Sock_wait > ..../SMPDU_Sock_wait > ....SOCK_OP_WRITE event.error = 0, result = 0, context=left > ....\smpd_handle_op_write > .....\smpd_state_writing_process_session_request > ......wrote process session request: 'process' > ......\SMPDU_Sock_post_read > .......\SMPDU_Sock_post_readv > ......./SMPDU_Sock_post_readv > ....../SMPDU_Sock_post_read > ...../smpd_state_writing_process_session_request > ..../smpd_handle_op_write > ....sock_waiting for the next event. > ....\SMPDU_Sock_wait > ..../SMPDU_Sock_wait > ....SOCK_OP_READ event.error = 0, result = 0, context=left > ....\smpd_handle_op_read > .....\smpd_state_reading_cred_request > ......read cred request: 'credentials' > ......\smpd_hide_string_arg > .......\first_token > ......./first_token > .......\compare_token > ......./compare_token > .......\next_token > ........\first_token > ......../first_token > ........\first_token > ......../first_token > ......./next_token > ....../smpd_hide_string_arg > ....../smpd_hide_string_arg > ......\smpd_hide_string_arg > .......\first_token > ......./first_token > .......\compare_token > ......./compare_token > .......\next_token > ........\first_token > ......../first_token > ........\first_token > ......../first_token > ......./next_token > ....../smpd_hide_string_arg > ....../smpd_hide_string_arg > ......\smpd_hide_string_arg > .......\first_token > ......./first_token > .......\compare_token > ......./compare_token > .......\next_token > ........\first_token > ......../first_token > ........\first_token > ......../first_token > ......./next_token > ....../smpd_hide_string_arg > ....../smpd_hide_string_arg > ......\smpd_hide_string_arg > .......\first_token > ......./first_token > .......\compare_token > ......./compare_token > .......\next_token > ........\first_token > ......../first_token > ........\first_token > ......../first_token > ......./next_token > ....../smpd_hide_string_arg > ....../smpd_hide_string_arg > ......\smpd_hide_string_arg > .......\first_token > ......./first_token > .......\compare_token > ......./compare_token > .......\next_token > ........\first_token > ......../first_token > ........\first_token > ......../first_token > ......./next_token > ....../smpd_hide_string_arg > ....../smpd_hide_string_arg > .......\smpd_option_on > ........\smpd_get_smpd_data > .........\smpd_get_smpd_data_from_environment > ........./smpd_get_smpd_data_from_environment > .........\smpd_get_smpd_data_default > ........./smpd_get_smpd_data_default > .........Unable to get the data for the key 'nocache' > ......../smpd_get_smpd_data > ......./smpd_option_on > ......\smpd_hide_string_arg > .......\first_token > ......./first_token > .......\compare_token > ......./compare_token > .......\next_token > ........\first_token > ......../first_token > ........\first_token > ......../first_token > ......./next_token > ....../smpd_hide_string_arg > ....../smpd_hide_string_arg > ......\SMPDU_Sock_post_write > .......\SMPDU_Sock_post_writev > ......./SMPDU_Sock_post_writev > ....../SMPDU_Sock_post_write > ...../smpd_handle_op_read > .....sock_waiting for the next event. > .....\SMPDU_Sock_wait > ...../SMPDU_Sock_wait > .....SOCK_OP_WRITE event.error = 0, result = 0, context=left > .....\smpd_handle_op_write > ......\smpd_state_writing_cred_ack_yes > .......wrote cred request yes ack. > .......\SMPDU_Sock_post_write > ........\SMPDU_Sock_post_writev > ......../SMPDU_Sock_post_writev > ......./SMPDU_Sock_post_write > ....../smpd_state_writing_cred_ack_yes > ...../smpd_handle_op_write > .....sock_waiting for the next event. > .....\SMPDU_Sock_wait > ...../SMPDU_Sock_wait > .....SOCK_OP_WRITE event.error = 0, result = 0, context=left > .....\smpd_handle_op_write > ......\smpd_state_writing_account > .......wrote account: 'Utilisateur' > .......\smpd_encrypt_data > ......./smpd_encrypt_data > .......\SMPDU_Sock_post_write > ........\SMPDU_Sock_post_writev > ......../SMPDU_Sock_post_writev > ......./SMPDU_Sock_post_write > ....../smpd_state_writing_account > ...../smpd_handle_op_write > .....sock_waiting for the next event. > .....\SMPDU_Sock_wait > ...../SMPDU_Sock_wait > .....SOCK_OP_WRITE event.error = 0, result = 0, context=left > .....\smpd_handle_op_write > ......\smpd_hide_string_arg > .......\first_token > ......./first_token > .......\compare_token > ......./compare_token > .......\next_token > ........\first_token > ......../first_token > ........\first_token > ......../first_token > ......./next_token > ....../smpd_hide_string_arg > ....../smpd_hide_string_arg > .......\smpd_hide_string_arg > ........\first_token > ......../first_token > ........\compare_token > ......../compare_token > ........\next_token > .........\first_token > ........./first_token > .........\first_token > ........./first_token > ......../next_token > ......./smpd_hide_string_arg > ......./smpd_hide_string_arg > .......\SMPDU_Sock_post_read > ........\SMPDU_Sock_post_readv > ......../SMPDU_Sock_post_readv > ......./SMPDU_Sock_post_read > ......\smpd_hide_string_arg > .......\first_token > ......./first_token > .......\compare_token > ......./compare_token > .......\next_token > ........\first_token > ......../first_token > ........\first_token > ......../first_token > ......./next_token > ....../smpd_hide_string_arg > ....../smpd_hide_string_arg > ...../smpd_handle_op_write > .....sock_waiting for the next event. > .....\SMPDU_Sock_wait > ...../SMPDU_Sock_wait > .....SOCK_OP_READ event.error = 0, result = 0, context=left > .....\smpd_handle_op_read > ......\smpd_state_reading_process_result > .......read process session result: 'FAIL' > .......\smpd_hide_string_arg > ........\first_token > ......../first_token > ........\compare_token > ......../compare_token > ........\next_token > .........\first_token > ........./first_token > .........\first_token > ........./first_token > ......../next_token > ......./smpd_hide_string_arg > ......./smpd_hide_string_arg > .......\smpd_hide_string_arg > ........\first_token > ......../first_token > ........\compare_token > ......../compare_token > ........\next_token > .........\first_token > ........./first_token > .........\first_token > ........./first_token > ......../next_token > ......./smpd_hide_string_arg > ......./smpd_hide_string_arg > Credentials for Utilisateur rejected connecting to Benoit > .......process session rejected > .......\SMPDU_Sock_post_close > ........\SMPDU_Sock_post_read > .........\SMPDU_Sock_post_readv > ........./SMPDU_Sock_post_readv > ......../SMPDU_Sock_post_read > ......./SMPDU_Sock_post_close > .......\smpd_post_abort_command > ........\smpd_create_command > .........\smpd_init_command > ........./smpd_init_command > ......../smpd_create_command > ........\smpd_add_command_arg > ......../smpd_add_command_arg > ........\smpd_command_destination > .........0 -> 0 : returning NULL context > ......../smpd_command_destination > Aborting: Unable to connect to Benoit > ......./smpd_post_abort_command > .......\smpd_exit > ........\smpd_kill_all_processes > ......../smpd_kill_all_processes > ........\smpd_finalize_drive_maps > ......../smpd_finalize_drive_maps > ........\smpd_dbs_finalize > ......../smpd_dbs_finalize > ........\SMPDU_Sock_finalize > ......../SMPDU_Sock_finalize > > C:\Users\Utilisateur> >> Hi, >> Looks like you missed the "-" before the status ("smpd -status" not >> "smpd status") argument. >> It also looks like you have multiple MPI libraries installed in your >> system. Try running this command (full path to mpiexec and smpd), >> >> # C:\Progra~1\MPICH2\bin\smpd -status >> >> # C:\Progra~1\MPICH2\bin\mpiexec -verbose -n 2 >> C:\Progra~1\MPICH2\examples\cpi.exe >> >> >> Regards, >> Jayesh >> >> ----- Original Message ----- >> From: "spatiogis" <geo(a)spatiogis.fr> >> To: "Jayesh Krishna" <jayesh(a)mcs.anl.gov> >> Sent: Friday, May 3, 2013 11:05:34 AM >> Subject: Re: [mpich-discuss] install + config on windows >> >> Hello, >> >> C:\Users\Utilisateur>smpd status >> Unexpected parameters: status >> >> C:\Users\Utilisateur>mpiexec -verbose -n 2 >> C:\Progra~1\MPICH2\examples\cpi.exe >> Unknown option: -verbose >> >> ----------------------------------------------------------------------------- >> C:\Program Files\MPICH2\examples>mpiexec -verbose -n 2 cpi.exe >> Unknown option: -verbose >> >> C:\Program Files\MPICH2\examples>smpd status >> Unexpected parameters: status >> ----------------------------------------------------------------------------- >> >> regards, Ben >> >>> Hi, >>> Ok. Please send us the output of the following commands, >>> >>> # smpd -status >>> # mpiexec -verbose -n 2 C:\Progra~1\MPICH2\examples\cpi.exe >>> >>> Please copy-paste the command and the complete output in your email. >>> >>> Regards, >>> Jayesh >>> >>> >>> ----- Original Message ----- >>> From: "spatiogis" <geo(a)spatiogis.fr> >>> To: discuss(a)mpich.org >>> Sent: Friday, May 3, 2013 1:46:53 AM >>> Subject: Re: [mpich-discuss] install + config on windows >>> >>> Hello >>> >>> >>>> (PS: I am assuming from your reply in the previous email that you can >>>> run a command like "mpiexec -n 2 C:\Progra~1\MPICH2\examples\cpi.exe" >>>> correctly) >>> >>> In fact this command doesn't run. >>> >>> The message is this one >>> >>> [01:11728]....ERROR:unable to read the cmd header on the pmi context, >>> Error = -1 >>> >>> Ben >>> >>> >>>> ----- Original Message ----- >>>> From: "spatiogis" <geo(a)spatiogis.fr> >>>> To: "Jayesh Krishna" <jayesh(a)mcs.anl.gov> >>>> Sent: Thursday, May 2, 2013 10:48:56 AM >>>> Subject: Re: [mpich-discuss] install + config on windows >>>> >>>> Hello, >>>> >>>>> Hi, >>>>> Are you able to run any other MPI programs? Try running the example >>>>> program, cpi.exe (C:\Program Files\MPICH2\examples\cpi.exe), to make >>>>> sure that your MPICH2 installation works. >>>> >>>> yes it does work >>>> >>>>> Installing MPICH2 on Windows 7 typically requires you to uninstall >>>>> any >>>>> previous versions of MPICH2, launch an administrative command promt >>>>> and >>>>> run "msiexec /i mpich2-installer.msi" to install MPICH2. >>>> >>>> yes it 's been installed like this... >>>> >>>> In wmpiconfig, the message is the following in the 'Get settings' >>>> line. >>>> >>>> Credentials for Utilisateur rejected connecting to host >>>> Aborting: Unable to connect to host >>>> >>>> The software I try to use is Taudem, which is intergrated inside >>>> Qgis. >>>> Launching a taudem process inside Qgis gives the same message. >>>> >>>> >>>>> Regards, >>>>> Jayesh >>>> >>>> Sincerely, Ben >>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: "spatiogis" <geo(a)spatiogis.fr> >>>>> To: discuss(a)mpich.org >>>>> Sent: Thursday, May 2, 2013 10:08:23 AM >>>>> Subject: Re: [mpich-discuss] install + config on windows >>>>> >>>>> Hello, >>>>> >>>>> in my case Mpich is normally used to run .exe programs. I guess that >>>>> they >>>>> are already compiled... >>>>> The .exe files are integrated into a software, and accessed from >>>>> menus >>>>> inside it. When I run one of the programs, the answer is actually >>>>> "unable >>>>> to query host". >>>>> At the end, the process is not realised. It seems that this 'host' >>>>> question is a problem to the software... >>>>> >>>>> Sincerely, >>>>> >>>>> Ben. >>>>> >>>>> >>>>>> Hi, >>>>>> You can download MPICH2 binaries for Windows at >>>>>> http://www.mpich.org/downloads/ . >>>>>> You need to compile your MPI programs with MPICH2 to make it work. >>>>>> I >>>>>> would recommend recompiling your code after you install MPICH2 (If >>>>>> you >>>>>> have MPI program binaries pre-built with MPICH2 - instead of >>>>>> compiling >>>>>> them on your own - make sure that you install the same version of >>>>>> MPICH2 >>>>>> that was used to build the binaries). >>>>>> The wmpiregister program has a bug and you can ignore this error >>>>>> message ("...unable to query host"). Can you run your MPI program >>>>>> using >>>>>> mpiexec from a command prompt? >>>>>> >>>>>> Regards, >>>>>> Jayesh >>>>>> >>>>>> ----- Original Message ----- >>>>>> From: "spatiogis" <geo(a)spatiogis.fr> >>>>>> To: discuss(a)mpich.org >>>>>> Sent: Tuesday, April 30, 2013 9:26:35 AM >>>>>> Subject: [mpich-discuss] install + config on windows >>>>>> >>>>>> Hello, >>>>>> >>>>>> I'm not very good at computing, but I would like to install Mpich2 >>>>>> on >>>>>> windows 7 - 64 bits. There is only one pc, with one user plus the >>>>>> admin, >>>>>> and a simple core processor. >>>>>> >>>>>> I would like to know if it's mandatory to have compiling softwares >>>>>> with >>>>>> it to make it work, whereas it is asked in this case only to make >>>>>> run >>>>>> another software, and not for compiling (that would maybe save some >>>>>> disk >>>>>> space and simplify the installation) ? >>>>>> >>>>>> My second issue is that I must be missing something about the >>>>>> server >>>>>> configuration. I have installed Mpich from the .msi file, then >>>>>> configured >>>>>> the wmpiregister program with the Domain/user informations. >>>>>> >>>>>> There is this message displayed when trying to connect in the >>>>>> 'configurable settings' window : 'MPICH2 not installed or unable to >>>>>> query >>>>>> the host'. >>>>>> >>>>>> What is the host actually ? >>>>>> >>>>>> I know I am starting from very far, I am sorry for these very >>>>>> simple >>>>>> questions. Thanks if you can reply me, that would certainly save me >>>>>> some >>>>>> long hours of reading and testing ;) >>>>>> >>>>>> sincerely, >>>>>> >>>>>> Ben >>>>>> _______________________________________________ >>>>>> discuss mailing list discuss(a)mpich.org >>>>>> To manage subscription options or unsubscribe: >>>>>> https://lists.mpich.org/mailman/listinfo/discuss >>>>> >>>>> >>>> >>>> >>> >>> >> >> > > -- Benoit Véler Adhérent au groupe JAM Ingénierie 180 Avenue du Genevois, Parc d'Activité de Croix Rousse 73000 Chambéry http://www.spatiogis.fr 06-46-13-40-94

1 0

Re: [mpich-discuss] Problems running MPICH jobs under SLURM
by Pavan Balaji 09 Jun '13

09 Jun '13

Excellent! Thanks for helping debug this. This fix will be available in the upcoming mpich-3.1b1 release. -- Pavan On 06/09/2013 03:09 PM, Biddiscombe, John A. wrote: > Pavan > > The words you wanted to see ... > > biddisco@breno2 ~/build/mpich-master-v3.0.4-294-ga5719ca8 $ salloc -N 1 -n2 > salloc: Granted job allocation 25 > biddisco@breno2 ~/build/mpich-master-v3.0.4-294-ga5719ca8 $ ./install/bin/mpiexec -n 2 ./hello > Hello world from process 0 of 2 > Hello world from process 1 of 2 > > Thank you very much indeed. Not only a very welcome fix, but done at the weekend too! > > Great work. Thanks again. > > JB > > > > > > -----Original Message----- > From: Pavan Balaji [mailto:[email protected]] > Sent: 09 June 2013 17:17 > To: Biddiscombe, John A. > Cc: discuss(a)mpich.org > Subject: Re: [mpich-discuss] Problems running MPICH jobs under SLURM > > > On 06/09/2013 01:03 AM, Biddiscombe, John A. wrote: >> For reasons unclear to me, With this tarball, I get no mpiexec compiled. >> >> I'm doing a diff between the latest tarballs and trying to find the problem ... >> >> JB >> >> ll install/bin/ >> total 68 >> lrwxrwxrwx 1 biddisco biddisco 6 Jun 9 07:55 mpic++ -> mpicxx >> -rwxr-xr-x 1 biddisco biddisco 9905 Jun 9 07:55 mpicc -rwxr-xr-x 1 >> biddisco biddisco 9300 Jun 9 07:55 mpichversion -rwxr-xr-x 1 >> biddisco biddisco 9458 Jun 9 07:55 mpicxx -rwxr-xr-x 1 biddisco >> biddisco 11551 Jun 9 07:55 mpif77 -rwxr-xr-x 1 biddisco biddisco >> 13375 Jun 9 07:55 mpif90 -rwxr-xr-x 1 biddisco biddisco 3430 Jun 9 >> 07:55 parkill > > Gah. Sorry about that. Can you try once more? > > http://www.mpich.org/static/tarballs/nightly/master/mpich/ > > -- Pavan > > -- > Pavan Balaji > http://www.mcs.anl.gov/~balaji > -- Pavan Balaji http://www.mcs.anl.gov/~balaji

1 0

Re: [mpich-discuss] Problems running MPICH jobs under SLURM
by Biddiscombe, John A. 09 Jun '13

09 Jun '13

Pavan The words you wanted to see ... biddisco@breno2 ~/build/mpich-master-v3.0.4-294-ga5719ca8 $ salloc -N 1 -n2 salloc: Granted job allocation 25 biddisco@breno2 ~/build/mpich-master-v3.0.4-294-ga5719ca8 $ ./install/bin/mpiexec -n 2 ./hello Hello world from process 0 of 2 Hello world from process 1 of 2 Thank you very much indeed. Not only a very welcome fix, but done at the weekend too! Great work. Thanks again. JB -----Original Message----- From: Pavan Balaji [mailto:[email protected]] Sent: 09 June 2013 17:17 To: Biddiscombe, John A. Cc: discuss(a)mpich.org Subject: Re: [mpich-discuss] Problems running MPICH jobs under SLURM On 06/09/2013 01:03 AM, Biddiscombe, John A. wrote: > For reasons unclear to me, With this tarball, I get no mpiexec compiled. > > I'm doing a diff between the latest tarballs and trying to find the problem ... > > JB > > ll install/bin/ > total 68 > lrwxrwxrwx 1 biddisco biddisco 6 Jun 9 07:55 mpic++ -> mpicxx > -rwxr-xr-x 1 biddisco biddisco 9905 Jun 9 07:55 mpicc -rwxr-xr-x 1 > biddisco biddisco 9300 Jun 9 07:55 mpichversion -rwxr-xr-x 1 > biddisco biddisco 9458 Jun 9 07:55 mpicxx -rwxr-xr-x 1 biddisco > biddisco 11551 Jun 9 07:55 mpif77 -rwxr-xr-x 1 biddisco biddisco > 13375 Jun 9 07:55 mpif90 -rwxr-xr-x 1 biddisco biddisco 3430 Jun 9 > 07:55 parkill Gah. Sorry about that. Can you try once more? http://www.mpich.org/static/tarballs/nightly/master/mpich/ -- Pavan -- Pavan Balaji http://www.mcs.anl.gov/~balaji

1 0

Re: [mpich-discuss] Problems running MPICH jobs under SLURM
by Pavan Balaji 09 Jun '13

09 Jun '13

On 06/09/2013 01:03 AM, Biddiscombe, John A. wrote: > For reasons unclear to me, With this tarball, I get no mpiexec compiled. > > I'm doing a diff between the latest tarballs and trying to find the problem ... > > JB > > ll install/bin/ > total 68 > lrwxrwxrwx 1 biddisco biddisco 6 Jun 9 07:55 mpic++ -> mpicxx > -rwxr-xr-x 1 biddisco biddisco 9905 Jun 9 07:55 mpicc > -rwxr-xr-x 1 biddisco biddisco 9300 Jun 9 07:55 mpichversion > -rwxr-xr-x 1 biddisco biddisco 9458 Jun 9 07:55 mpicxx > -rwxr-xr-x 1 biddisco biddisco 11551 Jun 9 07:55 mpif77 > -rwxr-xr-x 1 biddisco biddisco 13375 Jun 9 07:55 mpif90 > -rwxr-xr-x 1 biddisco biddisco 3430 Jun 9 07:55 parkill Gah. Sorry about that. Can you try once more? http://www.mpich.org/static/tarballs/nightly/master/mpich/ -- Pavan -- Pavan Balaji http://www.mcs.anl.gov/~balaji

1 0

Re: [mpich-discuss] Problems running MPICH jobs under SLURM
by Biddiscombe, John A. 09 Jun '13

09 Jun '13

For reasons unclear to me, With this tarball, I get no mpiexec compiled. I'm doing a diff between the latest tarballs and trying to find the problem ... JB ll install/bin/ total 68 lrwxrwxrwx 1 biddisco biddisco 6 Jun 9 07:55 mpic++ -> mpicxx -rwxr-xr-x 1 biddisco biddisco 9905 Jun 9 07:55 mpicc -rwxr-xr-x 1 biddisco biddisco 9300 Jun 9 07:55 mpichversion -rwxr-xr-x 1 biddisco biddisco 9458 Jun 9 07:55 mpicxx -rwxr-xr-x 1 biddisco biddisco 11551 Jun 9 07:55 mpif77 -rwxr-xr-x 1 biddisco biddisco 13375 Jun 9 07:55 mpif90 -rwxr-xr-x 1 biddisco biddisco 3430 Jun 9 07:55 parkill -----Original Message----- From: Pavan Balaji [mailto:[email protected]] Sent: 09 June 2013 07:13 To: discuss(a)mpich.org Cc: Biddiscombe, John A. Subject: Re: [mpich-discuss] Problems running MPICH jobs under SLURM John, Can you try the latest nightly snapshot? http://www.mpich.org/static/tarballs/nightly/master/mpich/ -- Pavan On 06/08/2013 03:23 PM, Pavan Balaji wrote: > > Thanks, John. I'll look into it and get back to you if I need any > more information. > > Btw, you should not need sudo at all. You might have some previously > left over files with root permissions that might have caused the issue. > If you delete the entire directory and start from scratch, this > issue should not be there. > > -- Pavan > > On 06/08/2013 03:02 PM, Biddiscombe, John A. wrote: >> Following your instructions (I only have 1 node, so changed N2 n4 to >> N >> 1 n2), same error, listed below... >> >> [NB . Only one interesting thing is that I cannot do a make as user >> biddisco and have to sudo make as it gives me some permission error >> otherwise mkdir -p >> '/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc' >> /usr/bin/install -c -m 644 src/env/mpicc.conf src/env/mpif77.conf >> src/env/mpif90.conf src/env/mpicxx.conf >> '/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc' >> /usr/bin/install: cannot remove >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpicc.conf': >> Permission denied >> /usr/bin/install: cannot remove >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpif77.conf': >> Permission denied >> /usr/bin/install: cannot remove >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpif90.conf': >> Permission denied >> /usr/bin/install: cannot remove >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpicxx.conf': >> Permission denied >> make[3]: *** [install-sysconfDATA] Error 1 >> make[3]: Leaving directory >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' >> make[2]: *** [install-am] Error 2 >> make[2]: Leaving directory >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' >> make[1]: *** [install-recursive] Error 1 >> make[1]: Leaving directory >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' >> make: *** [install] Error 2 >> ] >> >> JB >> >> biddisco@breno2 ~/build/mpich-master-v3.0.4-259-gf322ce79 $ >> ./install/bin/mpiexec -n 2 ./hello >> *** glibc detected *** ./hello: double free or corruption (fasttop): >> 0x00000000017b2340 *** >> ======= Backtrace: ========= >> /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fcaeb4a2b96] >> *** glibc detected *** ./hello: double free or corruption (fasttop): >> 0x00000000011e7340 *** >> ======= Backtrace: ========= >> /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fd1a77ddb96] >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10(MPIDI_Populate_vc_node_ids+0x3f9)[0x7fd1a7bc75a9] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10(MPID_Init+0x136)[0x7fd1a7bc1da6] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10(MPIR_Init_thread+0x22f)[0x7fd1a7c78f1f] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10(MPI_Init+0xae)[0x7fd1a7c788be] >> >> ./hello[0x40081e] >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10(MPIDI_Populate_vc_node_ids+0x3f9)[0x7fcaeb88c5a9] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10(MPID_Init+0x136)[0x7fcaeb886da6] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10(MPIR_Init_thread+0x22f)[0x7fcaeb93df1f] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10(MPI_Init+0xae)[0x7fcaeb93d8be] >> >> ./hello[0x40081e] >> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fcaeb44576 >> d] >> ./hello[0x400719] >> ======= Memory map: ======== >> 00400000-00401000 r-xp 00000000 08:01 >> 10625669 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello >> 00600000-00601000 r--p 00000000 08:01 >> 10625669 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello >> 00601000-00602000 rw-p 00001000 08:01 >> 10625669 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello >> 017b1000-017d2000 rw-p 00000000 00:00 >> 0 [heap] >> 7fcaeabe1000-7fcaeabe4000 rw-p 00000000 00:00 0 >> 7fcaeabe4000-7fcaeabf9000 r-xp 00000000 08:01 >> 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7fcaeabf9000-7fcaeadf8000 ---p 00015000 08:01 >> 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7fcaeadf8000-7fcaeadf9000 r--p 00014000 08:01 >> 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7fcaeadf9000-7fcaeadfa000 rw-p 00015000 08:01 >> 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7fcaeadfa000-7fcaeae12000 r-xp 00000000 08:01 >> 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so >> 7fcaeae12000-7fcaeb011000 ---p 00018000 08:01 >> 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so >> 7fcaeb011000-7fcaeb012000 r--p 00017000 08:01 >> 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so >> 7fcaeb012000-7fcaeb013000 rw-p 00018000 08:01 >> 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so >> 7fcaeb013000-7fcaeb017000 rw-p 00000000 00:00 0 >> 7fcaeb017000-7fcaeb01e000 r-xp 00000000 08:01 >> 9050343 /lib/x86_64-linux-gnu/librt-2.15.so >> 7fcaeb01e000-7fcaeb21d000 ---p 00007000 08:01 >> 9050343 /lib/x86_64-linux-gnu/librt-2.15.so >> 7fcaeb21d000-7fcaeb21e000 r--p 00006000 08:01 >> 9050343 /lib/x86_64-linux-gnu/librt-2.15.so >> 7fcaeb21e000-7fcaeb21f000 rw-p 00007000 08:01 >> 9050343 /lib/x86_64-linux-gnu/librt-2.15.so >> 7fcaeb21f000-7fcaeb223000 r-xp 00000000 08:01 >> 8661134 >> /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 >> 7fcaeb223000-7fcaeb422000 ---p 00004000 08:01 >> 8661134 >> /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 >> 7fcaeb422000-7fcaeb423000 r--p 00003000 08:01 >> 8661134 >> /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 >> 7fcaeb423000-7fcaeb424000 rw-p 00004000 08:01 >> 8661134 >> /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 >> 7fcaeb424000-7fcaeb5d9000 r-xp 00000000 08:01 >> 9050358 /lib/x86_64-linux-gnu/libc-2.15.so >> 7fcaeb5d9000-7fcaeb7d8000 ---p 001b5000 08:01 >> 9050358 /lib/x86_64-linux-gnu/libc-2.15.so >> 7fcaeb7d8000-7fcaeb7dc000 r--p 001b4000 08:01 >> 9050358 /lib/x86_64-linux-gnu/libc-2.15.so >> 7fcaeb7dc000-7fcaeb7de000 rw-p 001b8000 08:01 >> 9050358 /lib/x86_64-linux-gnu/libc-2.15.so >> 7fcaeb7de000-7fcaeb7e3000 rw-p 00000000 00:00 0 >> 7fcaeb7e3000-7fcaeba03000 r-xp 00000000 08:01 >> 11675463 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10.0.4 >> >> 7fcaeba03000-7fcaebc03000 ---p 00220000 08:01 >> 11675463 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10.0.4 >> >> 7fcaebc03000-7fcaebc10000 r--p 00220000 08:01 >> 11675463 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10.0.4 >> >> 7fcaebc10000-7fcaebc16000 rw-p 0022d000 08:01 >> 11675463 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10.0.4 >> >> 7fcaebc16000-7fcaebc4e000 rw-p 00000000 00:00 0 >> 7fcaebc4e000-7fcaebc70000 r-xp 00000000 08:01 >> 9050344 /lib/x86_64-linux-gnu/ld-2.15.so >> 7fcaebe54000-7fcaebe56000 rw-p 00000000 00:00 0 >> 7fcaebe6d000-7fcaebe70000 rw-p 00000000 00:00 0 >> 7fcaebe70000-7fcaebe71000 r--p 00022000 08:01 >> 9050344 /lib/x86_64-linux-gnu/ld-2.15.so >> 7fcaebe71000-7fcaebe73000 rw-p 00023000 08:01 >> 9050344 /lib/x86_64-linux-gnu/ld-2.15.so >> 7fff671e5000-7fff67206000 rw-p 00000000 00:00 >> 0 [stack] >> 7fff673b4000-7fff673b5000 r-xp 00000000 00:00 >> 0 [vdso] >> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 >> 0 [vsyscall] >> >> ===================================================================== >> ============== >> >> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES >> = EXIT CODE: 6 >> = CLEANING UP REMAINING PROCESSES >> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES >> ===================================================================== >> ============== >> >> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6) >> This typically refers to a problem with your application. >> Please see the FAQ page for debugging suggestions >> > -- Pavan Balaji http://www.mcs.anl.gov/~balaji

1 0

Re: [mpich-discuss] Problems running MPICH jobs under SLURM
by Pavan Balaji 09 Jun '13

09 Jun '13

John, Can you try the latest nightly snapshot? http://www.mpich.org/static/tarballs/nightly/master/mpich/ -- Pavan On 06/08/2013 03:23 PM, Pavan Balaji wrote: > > Thanks, John. I'll look into it and get back to you if I need any more > information. > > Btw, you should not need sudo at all. You might have some previously > left over files with root permissions that might have caused the issue. > If you delete the entire directory and start from scratch, this issue > should not be there. > > -- Pavan > > On 06/08/2013 03:02 PM, Biddiscombe, John A. wrote: >> Following your instructions (I only have 1 node, so changed N2 n4 to N >> 1 n2), same error, listed below... >> >> [NB . Only one interesting thing is that I cannot do a make as user >> biddisco and have to sudo make as it gives me some permission error >> otherwise >> mkdir -p >> '/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc' >> /usr/bin/install -c -m 644 src/env/mpicc.conf src/env/mpif77.conf >> src/env/mpif90.conf src/env/mpicxx.conf >> '/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc' >> /usr/bin/install: cannot remove >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpicc.conf': >> Permission denied >> /usr/bin/install: cannot remove >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpif77.conf': >> Permission denied >> /usr/bin/install: cannot remove >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpif90.conf': >> Permission denied >> /usr/bin/install: cannot remove >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpicxx.conf': >> Permission denied >> make[3]: *** [install-sysconfDATA] Error 1 >> make[3]: Leaving directory >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' >> make[2]: *** [install-am] Error 2 >> make[2]: Leaving directory >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' >> make[1]: *** [install-recursive] Error 1 >> make[1]: Leaving directory >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' >> make: *** [install] Error 2 >> ] >> >> JB >> >> biddisco@breno2 ~/build/mpich-master-v3.0.4-259-gf322ce79 $ >> ./install/bin/mpiexec -n 2 ./hello >> *** glibc detected *** ./hello: double free or corruption (fasttop): >> 0x00000000017b2340 *** >> ======= Backtrace: ========= >> /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fcaeb4a2b96] >> *** glibc detected *** ./hello: double free or corruption (fasttop): >> 0x00000000011e7340 *** >> ======= Backtrace: ========= >> /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fd1a77ddb96] >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIDI_Populate_vc_node_ids+0x3f9)[0x7fd1a7bc75a9] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPID_Init+0x136)[0x7fd1a7bc1da6] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIR_Init_thread+0x22f)[0x7fd1a7c78f1f] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPI_Init+0xae)[0x7fd1a7c788be] >> >> ./hello[0x40081e] >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIDI_Populate_vc_node_ids+0x3f9)[0x7fcaeb88c5a9] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPID_Init+0x136)[0x7fcaeb886da6] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIR_Init_thread+0x22f)[0x7fcaeb93df1f] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPI_Init+0xae)[0x7fcaeb93d8be] >> >> ./hello[0x40081e] >> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fcaeb44576d] >> ./hello[0x400719] >> ======= Memory map: ======== >> 00400000-00401000 r-xp 00000000 08:01 >> 10625669 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello >> 00600000-00601000 r--p 00000000 08:01 >> 10625669 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello >> 00601000-00602000 rw-p 00001000 08:01 >> 10625669 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello >> 017b1000-017d2000 rw-p 00000000 00:00 >> 0 [heap] >> 7fcaeabe1000-7fcaeabe4000 rw-p 00000000 00:00 0 >> 7fcaeabe4000-7fcaeabf9000 r-xp 00000000 08:01 >> 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7fcaeabf9000-7fcaeadf8000 ---p 00015000 08:01 >> 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7fcaeadf8000-7fcaeadf9000 r--p 00014000 08:01 >> 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7fcaeadf9000-7fcaeadfa000 rw-p 00015000 08:01 >> 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7fcaeadfa000-7fcaeae12000 r-xp 00000000 08:01 >> 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so >> 7fcaeae12000-7fcaeb011000 ---p 00018000 08:01 >> 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so >> 7fcaeb011000-7fcaeb012000 r--p 00017000 08:01 >> 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so >> 7fcaeb012000-7fcaeb013000 rw-p 00018000 08:01 >> 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so >> 7fcaeb013000-7fcaeb017000 rw-p 00000000 00:00 0 >> 7fcaeb017000-7fcaeb01e000 r-xp 00000000 08:01 >> 9050343 /lib/x86_64-linux-gnu/librt-2.15.so >> 7fcaeb01e000-7fcaeb21d000 ---p 00007000 08:01 >> 9050343 /lib/x86_64-linux-gnu/librt-2.15.so >> 7fcaeb21d000-7fcaeb21e000 r--p 00006000 08:01 >> 9050343 /lib/x86_64-linux-gnu/librt-2.15.so >> 7fcaeb21e000-7fcaeb21f000 rw-p 00007000 08:01 >> 9050343 /lib/x86_64-linux-gnu/librt-2.15.so >> 7fcaeb21f000-7fcaeb223000 r-xp 00000000 08:01 >> 8661134 >> /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 >> 7fcaeb223000-7fcaeb422000 ---p 00004000 08:01 >> 8661134 >> /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 >> 7fcaeb422000-7fcaeb423000 r--p 00003000 08:01 >> 8661134 >> /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 >> 7fcaeb423000-7fcaeb424000 rw-p 00004000 08:01 >> 8661134 >> /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 >> 7fcaeb424000-7fcaeb5d9000 r-xp 00000000 08:01 >> 9050358 /lib/x86_64-linux-gnu/libc-2.15.so >> 7fcaeb5d9000-7fcaeb7d8000 ---p 001b5000 08:01 >> 9050358 /lib/x86_64-linux-gnu/libc-2.15.so >> 7fcaeb7d8000-7fcaeb7dc000 r--p 001b4000 08:01 >> 9050358 /lib/x86_64-linux-gnu/libc-2.15.so >> 7fcaeb7dc000-7fcaeb7de000 rw-p 001b8000 08:01 >> 9050358 /lib/x86_64-linux-gnu/libc-2.15.so >> 7fcaeb7de000-7fcaeb7e3000 rw-p 00000000 00:00 0 >> 7fcaeb7e3000-7fcaeba03000 r-xp 00000000 08:01 >> 11675463 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 >> >> 7fcaeba03000-7fcaebc03000 ---p 00220000 08:01 >> 11675463 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 >> >> 7fcaebc03000-7fcaebc10000 r--p 00220000 08:01 >> 11675463 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 >> >> 7fcaebc10000-7fcaebc16000 rw-p 0022d000 08:01 >> 11675463 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 >> >> 7fcaebc16000-7fcaebc4e000 rw-p 00000000 00:00 0 >> 7fcaebc4e000-7fcaebc70000 r-xp 00000000 08:01 >> 9050344 /lib/x86_64-linux-gnu/ld-2.15.so >> 7fcaebe54000-7fcaebe56000 rw-p 00000000 00:00 0 >> 7fcaebe6d000-7fcaebe70000 rw-p 00000000 00:00 0 >> 7fcaebe70000-7fcaebe71000 r--p 00022000 08:01 >> 9050344 /lib/x86_64-linux-gnu/ld-2.15.so >> 7fcaebe71000-7fcaebe73000 rw-p 00023000 08:01 >> 9050344 /lib/x86_64-linux-gnu/ld-2.15.so >> 7fff671e5000-7fff67206000 rw-p 00000000 00:00 >> 0 [stack] >> 7fff673b4000-7fff673b5000 r-xp 00000000 00:00 >> 0 [vdso] >> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 >> 0 [vsyscall] >> >> =================================================================================== >> >> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES >> = EXIT CODE: 6 >> = CLEANING UP REMAINING PROCESSES >> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES >> =================================================================================== >> >> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6) >> This typically refers to a problem with your application. >> Please see the FAQ page for debugging suggestions >> > -- Pavan Balaji http://www.mcs.anl.gov/~balaji

1 0

Re: [mpich-discuss] Problems running MPICH jobs under SLURM
by Pavan Balaji 08 Jun '13

08 Jun '13

Thanks, John. I'll look into it and get back to you if I need any more information. Btw, you should not need sudo at all. You might have some previously left over files with root permissions that might have caused the issue. If you delete the entire directory and start from scratch, this issue should not be there. -- Pavan On 06/08/2013 03:02 PM, Biddiscombe, John A. wrote: > Following your instructions (I only have 1 node, so changed N2 n4 to N 1 n2), same error, listed below... > > [NB . Only one interesting thing is that I cannot do a make as user biddisco and have to sudo make as it gives me some permission error otherwise > mkdir -p '/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc' > /usr/bin/install -c -m 644 src/env/mpicc.conf src/env/mpif77.conf src/env/mpif90.conf src/env/mpicxx.conf '/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc' > /usr/bin/install: cannot remove `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpicc.conf': Permission denied > /usr/bin/install: cannot remove `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpif77.conf': Permission denied > /usr/bin/install: cannot remove `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpif90.conf': Permission denied > /usr/bin/install: cannot remove `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpicxx.conf': Permission denied > make[3]: *** [install-sysconfDATA] Error 1 > make[3]: Leaving directory `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' > make[2]: *** [install-am] Error 2 > make[2]: Leaving directory `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' > make[1]: *** [install-recursive] Error 1 > make[1]: Leaving directory `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' > make: *** [install] Error 2 > ] > > JB > > biddisco@breno2 ~/build/mpich-master-v3.0.4-259-gf322ce79 $ ./install/bin/mpiexec -n 2 ./hello > *** glibc detected *** ./hello: double free or corruption (fasttop): 0x00000000017b2340 *** > ======= Backtrace: ========= > /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fcaeb4a2b96] > *** glibc detected *** ./hello: double free or corruption (fasttop): 0x00000000011e7340 *** > ======= Backtrace: ========= > /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fd1a77ddb96] > /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIDI_Populate_vc_node_ids+0x3f9)[0x7fd1a7bc75a9] > /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPID_Init+0x136)[0x7fd1a7bc1da6] > /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIR_Init_thread+0x22f)[0x7fd1a7c78f1f] > /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPI_Init+0xae)[0x7fd1a7c788be] > ./hello[0x40081e] > /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIDI_Populate_vc_node_ids+0x3f9)[0x7fcaeb88c5a9] > /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPID_Init+0x136)[0x7fcaeb886da6] > /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIR_Init_thread+0x22f)[0x7fcaeb93df1f] > /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPI_Init+0xae)[0x7fcaeb93d8be] > ./hello[0x40081e] > /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fcaeb44576d] > ./hello[0x400719] > ======= Memory map: ======== > 00400000-00401000 r-xp 00000000 08:01 10625669 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello > 00600000-00601000 r--p 00000000 08:01 10625669 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello > 00601000-00602000 rw-p 00001000 08:01 10625669 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello > 017b1000-017d2000 rw-p 00000000 00:00 0 [heap] > 7fcaeabe1000-7fcaeabe4000 rw-p 00000000 00:00 0 > 7fcaeabe4000-7fcaeabf9000 r-xp 00000000 08:01 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 > 7fcaeabf9000-7fcaeadf8000 ---p 00015000 08:01 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 > 7fcaeadf8000-7fcaeadf9000 r--p 00014000 08:01 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 > 7fcaeadf9000-7fcaeadfa000 rw-p 00015000 08:01 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 > 7fcaeadfa000-7fcaeae12000 r-xp 00000000 08:01 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so > 7fcaeae12000-7fcaeb011000 ---p 00018000 08:01 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so > 7fcaeb011000-7fcaeb012000 r--p 00017000 08:01 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so > 7fcaeb012000-7fcaeb013000 rw-p 00018000 08:01 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so > 7fcaeb013000-7fcaeb017000 rw-p 00000000 00:00 0 > 7fcaeb017000-7fcaeb01e000 r-xp 00000000 08:01 9050343 /lib/x86_64-linux-gnu/librt-2.15.so > 7fcaeb01e000-7fcaeb21d000 ---p 00007000 08:01 9050343 /lib/x86_64-linux-gnu/librt-2.15.so > 7fcaeb21d000-7fcaeb21e000 r--p 00006000 08:01 9050343 /lib/x86_64-linux-gnu/librt-2.15.so > 7fcaeb21e000-7fcaeb21f000 rw-p 00007000 08:01 9050343 /lib/x86_64-linux-gnu/librt-2.15.so > 7fcaeb21f000-7fcaeb223000 r-xp 00000000 08:01 8661134 /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 > 7fcaeb223000-7fcaeb422000 ---p 00004000 08:01 8661134 /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 > 7fcaeb422000-7fcaeb423000 r--p 00003000 08:01 8661134 /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 > 7fcaeb423000-7fcaeb424000 rw-p 00004000 08:01 8661134 /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 > 7fcaeb424000-7fcaeb5d9000 r-xp 00000000 08:01 9050358 /lib/x86_64-linux-gnu/libc-2.15.so > 7fcaeb5d9000-7fcaeb7d8000 ---p 001b5000 08:01 9050358 /lib/x86_64-linux-gnu/libc-2.15.so > 7fcaeb7d8000-7fcaeb7dc000 r--p 001b4000 08:01 9050358 /lib/x86_64-linux-gnu/libc-2.15.so > 7fcaeb7dc000-7fcaeb7de000 rw-p 001b8000 08:01 9050358 /lib/x86_64-linux-gnu/libc-2.15.so > 7fcaeb7de000-7fcaeb7e3000 rw-p 00000000 00:00 0 > 7fcaeb7e3000-7fcaeba03000 r-xp 00000000 08:01 11675463 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 > 7fcaeba03000-7fcaebc03000 ---p 00220000 08:01 11675463 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 > 7fcaebc03000-7fcaebc10000 r--p 00220000 08:01 11675463 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 > 7fcaebc10000-7fcaebc16000 rw-p 0022d000 08:01 11675463 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 > 7fcaebc16000-7fcaebc4e000 rw-p 00000000 00:00 0 > 7fcaebc4e000-7fcaebc70000 r-xp 00000000 08:01 9050344 /lib/x86_64-linux-gnu/ld-2.15.so > 7fcaebe54000-7fcaebe56000 rw-p 00000000 00:00 0 > 7fcaebe6d000-7fcaebe70000 rw-p 00000000 00:00 0 > 7fcaebe70000-7fcaebe71000 r--p 00022000 08:01 9050344 /lib/x86_64-linux-gnu/ld-2.15.so > 7fcaebe71000-7fcaebe73000 rw-p 00023000 08:01 9050344 /lib/x86_64-linux-gnu/ld-2.15.so > 7fff671e5000-7fff67206000 rw-p 00000000 00:00 0 [stack] > 7fff673b4000-7fff673b5000 r-xp 00000000 00:00 0 [vdso] > ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] > > =================================================================================== > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = EXIT CODE: 6 > = CLEANING UP REMAINING PROCESSES > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > =================================================================================== > YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6) > This typically refers to a problem with your application. > Please see the FAQ page for debugging suggestions > -- Pavan Balaji http://www.mcs.anl.gov/~balaji

1 0

Re: [mpich-discuss] Problems running MPICH jobs under SLURM
by Biddiscombe, John A. 08 Jun '13

08 Jun '13

Following your instructions (I only have 1 node, so changed N2 n4 to N 1 n2), same error, listed below... [NB . Only one interesting thing is that I cannot do a make as user biddisco and have to sudo make as it gives me some permission error otherwise mkdir -p '/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc' /usr/bin/install -c -m 644 src/env/mpicc.conf src/env/mpif77.conf src/env/mpif90.conf src/env/mpicxx.conf '/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc' /usr/bin/install: cannot remove `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpicc.conf': Permission denied /usr/bin/install: cannot remove `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpif77.conf': Permission denied /usr/bin/install: cannot remove `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpif90.conf': Permission denied /usr/bin/install: cannot remove `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpicxx.conf': Permission denied make[3]: *** [install-sysconfDATA] Error 1 make[3]: Leaving directory `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' make: *** [install] Error 2 ] JB biddisco@breno2 ~/build/mpich-master-v3.0.4-259-gf322ce79 $ ./install/bin/mpiexec -n 2 ./hello *** glibc detected *** ./hello: double free or corruption (fasttop): 0x00000000017b2340 *** ======= Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fcaeb4a2b96] *** glibc detected *** ./hello: double free or corruption (fasttop): 0x00000000011e7340 *** ======= Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fd1a77ddb96] /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIDI_Populate_vc_node_ids+0x3f9)[0x7fd1a7bc75a9] /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPID_Init+0x136)[0x7fd1a7bc1da6] /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIR_Init_thread+0x22f)[0x7fd1a7c78f1f] /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPI_Init+0xae)[0x7fd1a7c788be] ./hello[0x40081e] /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIDI_Populate_vc_node_ids+0x3f9)[0x7fcaeb88c5a9] /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPID_Init+0x136)[0x7fcaeb886da6] /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIR_Init_thread+0x22f)[0x7fcaeb93df1f] /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPI_Init+0xae)[0x7fcaeb93d8be] ./hello[0x40081e] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fcaeb44576d] ./hello[0x400719] ======= Memory map: ======== 00400000-00401000 r-xp 00000000 08:01 10625669 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello 00600000-00601000 r--p 00000000 08:01 10625669 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello 00601000-00602000 rw-p 00001000 08:01 10625669 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello 017b1000-017d2000 rw-p 00000000 00:00 0 [heap] 7fcaeabe1000-7fcaeabe4000 rw-p 00000000 00:00 0 7fcaeabe4000-7fcaeabf9000 r-xp 00000000 08:01 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fcaeabf9000-7fcaeadf8000 ---p 00015000 08:01 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fcaeadf8000-7fcaeadf9000 r--p 00014000 08:01 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fcaeadf9000-7fcaeadfa000 rw-p 00015000 08:01 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fcaeadfa000-7fcaeae12000 r-xp 00000000 08:01 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fcaeae12000-7fcaeb011000 ---p 00018000 08:01 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fcaeb011000-7fcaeb012000 r--p 00017000 08:01 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fcaeb012000-7fcaeb013000 rw-p 00018000 08:01 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fcaeb013000-7fcaeb017000 rw-p 00000000 00:00 0 7fcaeb017000-7fcaeb01e000 r-xp 00000000 08:01 9050343 /lib/x86_64-linux-gnu/librt-2.15.so 7fcaeb01e000-7fcaeb21d000 ---p 00007000 08:01 9050343 /lib/x86_64-linux-gnu/librt-2.15.so 7fcaeb21d000-7fcaeb21e000 r--p 00006000 08:01 9050343 /lib/x86_64-linux-gnu/librt-2.15.so 7fcaeb21e000-7fcaeb21f000 rw-p 00007000 08:01 9050343 /lib/x86_64-linux-gnu/librt-2.15.so 7fcaeb21f000-7fcaeb223000 r-xp 00000000 08:01 8661134 /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 7fcaeb223000-7fcaeb422000 ---p 00004000 08:01 8661134 /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 7fcaeb422000-7fcaeb423000 r--p 00003000 08:01 8661134 /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 7fcaeb423000-7fcaeb424000 rw-p 00004000 08:01 8661134 /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 7fcaeb424000-7fcaeb5d9000 r-xp 00000000 08:01 9050358 /lib/x86_64-linux-gnu/libc-2.15.so 7fcaeb5d9000-7fcaeb7d8000 ---p 001b5000 08:01 9050358 /lib/x86_64-linux-gnu/libc-2.15.so 7fcaeb7d8000-7fcaeb7dc000 r--p 001b4000 08:01 9050358 /lib/x86_64-linux-gnu/libc-2.15.so 7fcaeb7dc000-7fcaeb7de000 rw-p 001b8000 08:01 9050358 /lib/x86_64-linux-gnu/libc-2.15.so 7fcaeb7de000-7fcaeb7e3000 rw-p 00000000 00:00 0 7fcaeb7e3000-7fcaeba03000 r-xp 00000000 08:01 11675463 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 7fcaeba03000-7fcaebc03000 ---p 00220000 08:01 11675463 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 7fcaebc03000-7fcaebc10000 r--p 00220000 08:01 11675463 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 7fcaebc10000-7fcaebc16000 rw-p 0022d000 08:01 11675463 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 7fcaebc16000-7fcaebc4e000 rw-p 00000000 00:00 0 7fcaebc4e000-7fcaebc70000 r-xp 00000000 08:01 9050344 /lib/x86_64-linux-gnu/ld-2.15.so 7fcaebe54000-7fcaebe56000 rw-p 00000000 00:00 0 7fcaebe6d000-7fcaebe70000 rw-p 00000000 00:00 0 7fcaebe70000-7fcaebe71000 r--p 00022000 08:01 9050344 /lib/x86_64-linux-gnu/ld-2.15.so 7fcaebe71000-7fcaebe73000 rw-p 00023000 08:01 9050344 /lib/x86_64-linux-gnu/ld-2.15.so 7fff671e5000-7fff67206000 rw-p 00000000 00:00 0 [stack] 7fff673b4000-7fff673b5000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 6 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES =================================================================================== YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6) This typically refers to a problem with your application. Please see the FAQ page for debugging suggestions

1 0

Re: [mpich-discuss] crash on 2^31 size in MPI_Win_allocate_shared(...)
by Weise Steffen 08 Jun '13

08 Jun '13

Dear Jeff, thanks for taking care of the issue. Sure your right about the signed vs. unsigned int stuff but i also tried it with long int : same result. Every integer in my code (memory manager) is long unsigned int, no reason to deal with negative sizes (at least from my perspective). I have an extended version of this example which actually uses the window, sets it and checks it afterwards (but didn't post it to keep the source file small, also the issue is not with that part of the code). All sizes not exactly equal to 2^31 and some multiples of that work very well and "df -h" on /dev/shm clearly shows that it is used correctly. Memory sizes returned by MPI_Win_shared_query also match the requested amount. my installation is in /opt/mpi/ (which would mean i consider MPICH to be THE MPI) ;) I still have to rename my source repo ~/git/openmpi though ;) regards, Steffen Weise First, "long unsigned int window_size=2147483648" is not correct. They type you need to use there is MPI_Aint. The syntax of this function is int MPI_Win_allocate_shared(MPI_Aint size, int disp_unit, MPI_Info info, MPI_Comm comm, void *baseptr, MPI_Win *win) It may be true that "long unsigned int" is safely case to MPI_Aint, but that's a very danger way to write code and it may be broken on some platforms. In any case, everything above 2^31 is probably not okay. Unless absolutely every integer type used in the code paths you are hitting is size_t (or equivalent) and not int, you're going to hit overflow somewhere. Maybe I'm wrong, but you should verify (as a debugging mechanism, not in general) that MPI_Win_allocate_shared is behaving as desired by memset-ing the resulting data (mem) to verify that you're actually getting e.g. 2^34 bytes back. If /dev/shm is 4G, I'm not sure how that's possible but maybe the implementation doesn't use that. I'm going to be on a plane today but I'll run your code on my machine and try to figure out more about how "count-safe" MPI_Win_allocate_shared is. Jeff PS Installing MPICH in ~/git/openmpi is just dirty :-) On Fri, Jun 7, 2013 at 5:50 AM, Weise Steffen <Steffen.Weise(a)iec.tu-freiberg.de<mailto:[email protected]>> wrote: Dear mailing-list, this is my first time posting here. I found that with version 3.0.4 using MPI_Win_allocate_shared i get an error when using a size exactly 2^31 everything below and above is ok. Though i also had the same issue with 2^34. Some kind of division or type conversion seems to be off. (/dev/shm has 4G so it is not a size issue.. i know what those errors look like) I attach my code and the output i get on a linux (debian 6.0) 64 bit machine (same issue on a mac though) . I'll be happy to provide more machine details or everything you guys need to analyse whats going on. with kind regards, Steffen Weise _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

1 0

Re: [mpich-discuss] Porting MPICH
by Pavan Balaji 07 Jun '13

07 Jun '13

On 06/07/2013 10:10 PM, Jeff Hammond wrote: > I looked into this more thoroughly. The simple solution is to use > "--with-thread-package=no --enable-threads=single" together. The > latter will disable the use of all thread-related functions that lead > to missing symbols due to the former. > > In short, a no-op implementation is not necessary, as I found out > _after_ I had created one. I've committed a patch into mpich/master to throw an error if this happens. -- Pavan -- Pavan Balaji http://www.mcs.anl.gov/~balaji

1 0