From mondelli at ill.fr Tue Apr 17 16:12:14 2012 From: mondelli at ill.fr (MONDELLI) Date: Tue, 17 Apr 2012 16:12:14 +0200 Subject: [mcstas-users] Postdoc position available in Grenoble Message-ID: <7468E084-EEA5-487D-9F00-80EE675F2D6A@ill.fr> Postdoctoral position (assegno di ricerca) is available at OGG-CNR in Grenoble Title: "Study by ray tracing techniques to develop polarization of neutron for the European Spallation Source". Field: Physics, Neutron Polarization, Ray tracing Candidate: - University degree with a PhD in one of these fields: Physics, Chemistry, Electronic Engineering, Nuclear Engineering, Chemistry and Materials engineering, Material Science. - two years of experience in the topic - fluent english - basic italian Application: Before 24th of april 2012. Application, form, conditions, and details available on the website of the CNR: http://bandi.urp.cnr.it/assegni/faces/pubblica/RisultatoCercaAssegniPubblica.jsp Code: Codice Bando ISM-001-2012-RM, scadenza : 24/04/2012 (warming: the application form is in italian) If you need more informations please do not hesitate to contact me by email. Claudia Mondelli Dr. Claudia Mondelli Time of Flight/High Resolution CNR-IOM-OGG Institut Laue Langevin 6, Rue Jules Horowitz F-38042 Grenoble Cedex 9 France Tel. +33.476.20.7350 Fax. +33.476.20.7688 -------------- next part -------------- An HTML attachment was scrubbed... URL: From pkwi at fysik.dtu.dk Wed May 9 22:28:03 2012 From: pkwi at fysik.dtu.dk (=?utf-8?B?UGV0ZXIgS2rDpnIgV2lsbGVuZHJ1cA==?=) Date: Wed, 9 May 2012 22:28:03 +0200 Subject: [mcstas-users] ESS DMSC vacancy in scientific software development Message-ID: <630BD8E4-E1D4-4B0F-A3D1-2E7B8BB4B255@fysik.dtu.dk> Hello everyone, The interim ESS DMSC (Data Management and Software Center for the European Spallation Source) located at the Niels Bohr Institute, University of Copenhagen is seeking a candidate for scientific software development within areas of data analysis and simulation. Please find attached the related advert. Applications should be submitted through this link: https://ssl1.peoplexs.com/Peoplexs22/CandidatesPortalNoLogin/Vacancy.cfm?PortalID=3417&VacatureID=241334&BedrijfID=0&Vacancy=Scientific%20software%20development%20#top For further questions or enquiries, please contact Prof. Stig Skelboe, Niels Bohr Institute, University of Copenhagen, skelboe at nbi.dk, phone +45 35321449 Best regards, Peter Willendrup Peter Kj?r Willendrup Development engineer DTU Physics [cid:3e2eae4c-898f-453e-857a-170b64da4f87 at win.dtu.dk] Technical University of Denmark [cid:4af7bbe2-eb0d-4d68-b589-e4081ffd64a2 at win.dtu.dk] Department of Physics Fysikvej Building 307 DK-2800 Kongens Lyngby Direct +45 2125 4612 Mobil +45 2125 4612 Fax +45 4593 2399 pkwi at fysik.dtu.dk -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... 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Name: Scientific software development.pdf Type: application/pdf Size: 69364 bytes Desc: Scientific software development.pdf URL: From riamounia at yahoo.fr Thu May 31 13:21:26 2012 From: riamounia at yahoo.fr (fatma riahi) Date: Thu, 31 May 2012 12:21:26 +0100 (BST) Subject: [mcstas-users] Question Message-ID: <1338463286.11744.YahooMailClassic@web28801.mail.ir2.yahoo.com> Dear I work as a beginner on the simulation of the diffractometer of two axes installed around ES-Salam reactor (Algeria) by using program Mcstas, I inform you that the details of the diffractometer are published on the journal Radioanal Nucl Chem entitled : ?New determination method of the neutron diffraction system resolution at the Algerian Es-Salam research reactor ? I thus come to expose you my problem relating to the simulation of the cylindrical detector which moves during the experiment step by step and in each step it collects the intensity for one fixed duration ,I would be very grateful if you could help me to solve this problem.Thank you in advance Sincerely yours Riahi From farhi at ill.eu Thu May 31 16:51:59 2012 From: farhi at ill.eu (Emmanuel FARHI) Date: Thu, 31 May 2012 16:51:59 +0200 Subject: [mcstas-users] NMI3/ILL LiveDVD with many pre-installed neutron software (12.04) Message-ID: <4FC7858F.5010500@ill.eu> An HTML attachment was scrubbed... URL: From Jean-Francois.Moulin at hzg.de Wed Jun 13 17:36:37 2012 From: Jean-Francois.Moulin at hzg.de (Jean-Francois.Moulin at hzg.de) Date: Wed, 13 Jun 2012 17:36:37 +0200 Subject: [mcstas-users] openmpi compilation problem Message-ID: Hi to all! new Linux distro, new problem! On Linux Mint 13 I do not manage to install due to mpi problems. As already suggested some months ago I installed openmpi (packages from Ubuntu repos: libopenmpi 1.4.3.2 and its dev). The ./configure tells me that : checking mpi.h presence... no checking for mpi.h... no WARNING: /usr/bin/mpicc may fail to compile without mpi.h but I find this on my system: ./usr/lib/openmpi/include/mpi.h After reading the output of configure -h, I tried ./configure -I/usr/lib/openmpi/include/: configure: error: unrecognized option: `-I' I tried putting this path in the cppflags envirt variable. To no avail. seems I miss the point. Since I get a Makefile I looked for an include section where I could manually put the path but that does not look so easy... (for me) second question I am on a 64 bit machine, I should thus configure --with-pic right? Thanks in advance for your help! Best Jean-Francois - Helmholtz Zentrum Geesthacht Institut f?r Werkstoffforschung Abteilung WPN, Instrument REFSANS Lichtenbergstr. 1 85747 Garching FRM II Tel.: +49 (0)89 289 10762 Internet: http://www.frm2.tum.deHelmholtz-Zentrum Geesthacht Zentrum f?r Material- und K?stenforschung GmbH Max-Planck-Stra?e 1 I 21502 Geesthacht I Deutschland/Germany Gesch?ftsf?hrer/Board of Management: Prof. Dr. Wolfgang Kaysser, Dipl.-Ing. Michael Gan? Vorsitzender des Aufsichtsrates/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Amtsgericht L?beck HRB 285 GE (Register Court) Internet: http://www.hzg.de From farhi at ill.eu Thu Jun 14 10:15:28 2012 From: farhi at ill.eu (Emmanuel FARHI) Date: Thu, 14 Jun 2012 10:15:28 +0200 Subject: [mcstas-users] openmpi compilation problem In-Reply-To: References: Message-ID: <4FD99DA0.1040909@ill.eu> Hi Jean-Francois, to my knowledge, this is just a warning. The tar.gz configure; make; make install should proceed OK still, and McStas should be able to find MPI if 'mpicc' and 'mpirun' commands are available at the prompt. OpenMPI seems OK on recent systems. It was less reliable than MPICH until 2010-2011 (would stall for long simulations with e.g. ncount > 2e9). Emmanuel. On 06/13/2012 05:36 PM, Jean-Francois.Moulin at hzg.de wrote: > Hi to all! > > new Linux distro, new problem! On Linux Mint 13 I do not manage to install due to mpi problems. As already suggested some months ago I installed openmpi (packages from Ubuntu repos: libopenmpi 1.4.3.2 and its dev). > The ./configure tells me that : > checking mpi.h presence... no > checking for mpi.h... no > WARNING: /usr/bin/mpicc may fail to compile without mpi.h > > but I find this on my system: > ./usr/lib/openmpi/include/mpi.h > After reading the output of configure -h, I tried > ./configure -I/usr/lib/openmpi/include/: > configure: error: unrecognized option: `-I' > I tried putting this path in the cppflags envirt variable. To no avail. > seems I miss the point. > Since I get a Makefile I looked for an include section where I could manually put the path but that does not look so easy... (for me) > > second question I am on a 64 bit machine, I should thus configure --with-pic right? > > Thanks in advance for your help! > > Best > > Jean-Francois > > > - > Helmholtz Zentrum Geesthacht > Institut f?r Werkstoffforschung > Abteilung WPN, Instrument REFSANS > Lichtenbergstr. 1 > 85747 Garching FRM II > Tel.: +49 (0)89 289 10762 > Internet: http://www.frm2.tum.deHelmholtz-Zentrum Geesthacht > Zentrum f?r Material- und K?stenforschung GmbH > Max-Planck-Stra?e 1 I 21502 Geesthacht I Deutschland/Germany > > Gesch?ftsf?hrer/Board of Management: Prof. Dr. Wolfgang Kaysser, Dipl.-Ing. Michael Gan? > Vorsitzender des Aufsichtsrates/Chairman of the Supervisory Board: MinDirig Wilfried Kraus > Amtsgericht L?beck HRB 285 GE (Register Court) > Internet: http://www.hzg.de > _______________________________________________ > mcstas-users mailing list > mcstas-users at mcstas.org > http://mailman.mcstas.org/cgi-bin/mailman/listinfo/mcstas-users -- Emmanuel FARHI,www.ill.eu/computing/people/emmanuel-farhi \|/ ____ \|/ CS-Group ILL4/221, Institut Laue-Langevin (ILL) Grenoble ~@-/ oO \-@~ 6 rue J. Horowitz, BP 156, 38042 Grenoble Cedex 9,France /_( \__/ )_\ Work :Tel (33/0) 4 76 20 71 35. Fax (33/0) 4 76 48 39 06 \__U_/ From Jean-Francois.Moulin at hzg.de Thu Jun 14 13:49:56 2012 From: Jean-Francois.Moulin at hzg.de (Jean-Francois.Moulin at hzg.de) Date: Thu, 14 Jun 2012 13:49:56 +0200 Subject: [mcstas-users] openmpi compilation problem In-Reply-To: <4FD99DA0.1040909@ill.eu> References: <4FD99DA0.1040909@ill.eu>, Message-ID: Hi Emmanuel! thanks for the answer. Yes the build works but, this is what I get when I try to use it: (case A) ~/Lab/MCarlo/McStas$ mcgui refsans_simplified_0.instr ./refsans_simplified_0.out: error while loading shared libraries: libmpich.so.3: cannot open shared object file: No such file or directory And this is correct, the file is not on my system... why did the configure look for mpich in the first place? (caseB) Well it wants MPICH? I tried and installed mpich2 from ubuntu repos (including dev), ./configure make make install... mcgui now starts without problem and shows my instrument parameters (it did not in case A) but the simulation returns errors... mcrun: No MPI/grid machine list. Running locally. Define /home/jfmoulin/.mcstas/hosts or /usr/local/lib/mcstas/tools/perl/hosts or use option --machines= [jfm-lap:11887] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 357 [jfm-lap:11887] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 230 [jfm-lap:11887] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../orte/runtime/orte_init.c at line 132 -------------------------------------------------------------------------- It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): orte_ess_set_name failed --> Returned value A system-required executable either could not be found or was not executable by this user (-127) instead of ORTE_SUCCESS Is there a reason to have conflicts between the two mpi (I have dependencies of other packages on openmpi) or do I forget a setup step? I had the box running before and did not change my home dir so I guess it should still work Anyway, thanks for your help! Ciao JF - Helmholtz Zentrum Geesthacht Institut f?r Werkstoffforschung Abteilung WPN, Instrument REFSANS Lichtenbergstr. 1 85747 Garching FRM II Tel.: +49 (0)89 289 10762 Internet: http://www.frm2.tum.de -----Emmanuel FARHI schrieb: ----- An: Jean-Francois.Moulin at hzg.de, "McStas users list at mcstas.org" Von: Emmanuel FARHI Datum: 06/14/2012 10:22AM Betreff: Re: [mcstas-users] openmpi compilation problem Hi Jean-Francois, to my knowledge, this is just a warning. The tar.gz configure; make; make install should proceed OK still, and McStas should be able to find MPI if 'mpicc' and 'mpirun' commands are available at the prompt. OpenMPI seems OK on recent systems. It was less reliable than MPICH until 2010-2011 (would stall for long simulations with e.g. ncount > 2e9). Emmanuel. On 06/13/2012 05:36 PM, Jean-Francois.Moulin at hzg.de wrote: > Hi to all! > > new Linux distro, new problem! On Linux Mint 13 I do not manage to install due to mpi problems. As already suggested some months ago I installed openmpi (packages from Ubuntu repos: libopenmpi 1.4.3.2 and its dev). > The ./configure tells me that : > checking mpi.h presence... no > checking for mpi.h... no > WARNING: /usr/bin/mpicc may fail to compile without mpi.h > > but I find this on my system: > ./usr/lib/openmpi/include/mpi.h > After reading the output of configure -h, I tried > ? ./configure -I/usr/lib/openmpi/include/: > configure: error: unrecognized option: `-I' > I tried putting this path in the cppflags envirt variable. To no avail. > seems I miss the point. > Since I get a Makefile I looked for an include section where I could manually put the path but that does not look so easy... (for me) > > second question I am on a 64 bit machine, I should thus configure --with-pic right? > > Thanks in advance for your help! > > Best > > Jean-Francois > > > - > Helmholtz Zentrum Geesthacht > Institut f?r Werkstoffforschung > Abteilung WPN, Instrument REFSANS > Lichtenbergstr. 1 > 85747 Garching FRM II > Tel.: +49 (0)89 289 10762 > Internet: http://www.frm2.tum.deHelmholtz-Zentrum?Geesthacht > Zentrum f?r Material- und K?stenforschung GmbH > Max-Planck-Stra?e 1 I 21502 Geesthacht I Deutschland/Germany > > Gesch?ftsf?hrer/Board of Management: Prof. Dr. Wolfgang Kaysser, Dipl.-Ing. Michael Gan? > Vorsitzender des Aufsichtsrates/Chairman of the Supervisory Board: MinDirig Wilfried Kraus > Amtsgericht L?beck HRB 285 GE (Register Court) > Internet: http://www.hzg.de > _______________________________________________ > mcstas-users mailing list > mcstas-users at mcstas.org > http://mailman.mcstas.org/cgi-bin/mailman/listinfo/mcstas-users -- Emmanuel FARHI,www.ill.eu/computing/people/emmanuel-farhi \|/ ____ \|/ CS-Group ILL4/221, Institut Laue-Langevin (ILL) Grenoble ?~@-/ oO \-@~ 6 rue J. Horowitz, BP 156, 38042 Grenoble Cedex 9,France ?/_( \__/ )_\ Work :Tel (33/0) 4 76 20 71 35. Fax (33/0) 4 76 48 39 06 ? ? \__U_/ Helmholtz-Zentrum Geesthacht Zentrum f?r Material- und K?stenforschung GmbH Max-Planck-Stra?e 1 I 21502 Geesthacht I Deutschland/Germany Gesch?ftsf?hrer/Board of Management: Prof. Dr. Wolfgang Kaysser, Dipl.-Ing. Michael Gan? Vorsitzender des Aufsichtsrates/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Amtsgericht L?beck HRB 285 GE (Register Court) Internet: http://www.hzg.de From pkwi at fysik.dtu.dk Thu Jun 14 13:59:45 2012 From: pkwi at fysik.dtu.dk (=?Windows-1252?Q?Peter_Kj=E6r_Willendrup?=) Date: Thu, 14 Jun 2012 13:59:45 +0200 Subject: [mcstas-users] openmpi compilation problem In-Reply-To: References: <4FD99DA0.1040909@ill.eu>, Message-ID: <0425F06D-3029-4FF8-8450-7460906F2489@fysik.dtu.dk> Hi Jean-Francois, Yup, you certainly have a conflict between your two MPI's now? :-) What does your mpirun / mpicc lines in /usr/local/lib/mcstas/tools/perl/mcstas_config.perl say? (I.e. MPIRUN => '/usr/local/bin/mpirun', MPICC => '/usr/local/bin/mpicc', ) Also, check if you perhaps have a .mcstas/mcstas_config.perl in your homedir? Best, Peter On Jun 14, 2012, at 13:49 , > wrote: Hi Emmanuel! thanks for the answer. Yes the build works but, this is what I get when I try to use it: (case A) ~/Lab/MCarlo/McStas$ mcgui refsans_simplified_0.instr ./refsans_simplified_0.out: error while loading shared libraries: libmpich.so.3: cannot open shared object file: No such file or directory And this is correct, the file is not on my system... why did the configure look for mpich in the first place? (caseB) Well it wants MPICH? I tried and installed mpich2 from ubuntu repos (including dev), ./configure make make install... mcgui now starts without problem and shows my instrument parameters (it did not in case A) but the simulation returns errors... mcrun: No MPI/grid machine list. Running locally. Define /home/jfmoulin/.mcstas/hosts or /usr/local/lib/mcstas/tools/perl/hosts or use option --machines= [jfm-lap:11887] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 357 [jfm-lap:11887] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 230 [jfm-lap:11887] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../orte/runtime/orte_init.c at line 132 -------------------------------------------------------------------------- It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): orte_ess_set_name failed --> Returned value A system-required executable either could not be found or was not executable by this user (-127) instead of ORTE_SUCCESS Is there a reason to have conflicts between the two mpi (I have dependencies of other packages on openmpi) or do I forget a setup step? I had the box running before and did not change my home dir so I guess it should still work Anyway, thanks for your help! Ciao JF - Helmholtz Zentrum Geesthacht Institut f?r Werkstoffforschung Abteilung WPN, Instrument REFSANS Lichtenbergstr. 1 85747 Garching FRM II Tel.: +49 (0)89 289 10762 Internet: http://www.frm2.tum.de -----Emmanuel FARHI > schrieb: ----- An: Jean-Francois.Moulin at hzg.de, "McStas users list at mcstas.org" > Von: Emmanuel FARHI > Datum: 06/14/2012 10:22AM Betreff: Re: [mcstas-users] openmpi compilation problem Hi Jean-Francois, to my knowledge, this is just a warning. The tar.gz configure; make; make install should proceed OK still, and McStas should be able to find MPI if 'mpicc' and 'mpirun' commands are available at the prompt. OpenMPI seems OK on recent systems. It was less reliable than MPICH until 2010-2011 (would stall for long simulations with e.g. ncount > 2e9). Emmanuel. On 06/13/2012 05:36 PM, Jean-Francois.Moulin at hzg.de wrote: Hi to all! new Linux distro, new problem! On Linux Mint 13 I do not manage to install due to mpi problems. As already suggested some months ago I installed openmpi (packages from Ubuntu repos: libopenmpi 1.4.3.2 and its dev). The ./configure tells me that : checking mpi.h presence... no checking for mpi.h... no WARNING: /usr/bin/mpicc may fail to compile without mpi.h but I find this on my system: ./usr/lib/openmpi/include/mpi.h After reading the output of configure -h, I tried ./configure -I/usr/lib/openmpi/include/: configure: error: unrecognized option: `-I' I tried putting this path in the cppflags envirt variable. To no avail. seems I miss the point. Since I get a Makefile I looked for an include section where I could manually put the path but that does not look so easy... (for me) second question I am on a 64 bit machine, I should thus configure --with-pic right? Thanks in advance for your help! Best Jean-Francois - Helmholtz Zentrum Geesthacht Institut f?r Werkstoffforschung Abteilung WPN, Instrument REFSANS Lichtenbergstr. 1 85747 Garching FRM II Tel.: +49 (0)89 289 10762 Internet: http://www.frm2.tum.deHelmholtz-Zentrum Geesthacht Zentrum f?r Material- und K?stenforschung GmbH Max-Planck-Stra?e 1 I 21502 Geesthacht I Deutschland/Germany Gesch?ftsf?hrer/Board of Management: Prof. Dr. Wolfgang Kaysser, Dipl.-Ing. Michael Gan? Vorsitzender des Aufsichtsrates/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Amtsgericht L?beck HRB 285 GE (Register Court) Internet: http://www.hzg.de _______________________________________________ mcstas-users mailing list mcstas-users at mcstas.org http://mailman.mcstas.org/cgi-bin/mailman/listinfo/mcstas-users -- Emmanuel FARHI,www.ill.eu/computing/people/emmanuel-farhi \|/ ____ \|/ CS-Group ILL4/221, Institut Laue-Langevin (ILL) Grenoble ~@-/ oO \-@~ 6 rue J. Horowitz, BP 156, 38042 Grenoble Cedex 9,France /_( \__/ )_\ Work :Tel (33/0) 4 76 20 71 35. Fax (33/0) 4 76 48 39 06 \__U_/ Helmholtz-Zentrum Geesthacht Zentrum f?r Material- und K?stenforschung GmbH Max-Planck-Stra?e 1 I 21502 Geesthacht I Deutschland/Germany Gesch?ftsf?hrer/Board of Management: Prof. Dr. Wolfgang Kaysser, Dipl.-Ing. Michael Gan? Vorsitzender des Aufsichtsrates/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Amtsgericht L?beck HRB 285 GE (Register Court) Internet: http://www.hzg.de _______________________________________________ mcstas-users mailing list mcstas-users at mcstas.org http://mailman.mcstas.org/cgi-bin/mailman/listinfo/mcstas-users Peter Kj?r Willendrup Development engineer DTU Physics Technical University of Denmark [cid:image002.gif at 01CCCAF1.5E6331F0] Department of Physics Fysikvej Building 307 DK-2800 Kongens Lyngby Direct +45 2125 4612 Mobil +45 2125 4612 Fax +45 4593 2399 pkwi at fysik.dtu.dk -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.gif Type: image/gif Size: 58 bytes Desc: image001.gif URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.gif Type: image/gif Size: 1055 bytes Desc: image002.gif URL: From farhi at ill.eu Thu Jun 14 17:35:48 2012 From: farhi at ill.eu (Emmanuel FARHI) Date: Thu, 14 Jun 2012 17:35:48 +0200 Subject: [mcstas-users] question 'auto time' in nD_monitor In-Reply-To: <62D53FDB-74F3-454F-A1BF-43646D809B72@fysik.dtu.dk> References: <8391107F-B245-4D49-BCC1-F266BDA7CB75@fysik.dtu.dk>, <5FB00A35-0D14-4DA7-AD64-C4DE975FFB95@fysik.dtu.dk> <62D53FDB-74F3-454F-A1BF-43646D809B72@fysik.dtu.dk> Message-ID: <4FDA04D4.5030506@ill.eu> An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/gif Size: 58 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/gif Size: 1055 bytes Desc: not available URL: From farhi at ill.eu Thu Jun 14 17:56:24 2012 From: farhi at ill.eu (Emmanuel FARHI) Date: Thu, 14 Jun 2012 17:56:24 +0200 Subject: [mcstas-users] openmpi compilation problem In-Reply-To: References: <4FD99DA0.1040909@ill.eu>, Message-ID: <4FDA09A8.1020605@ill.eu> Yes, you probably have conflicts between the two MPI packages. I would recommend to suppress MPICH2, which requires a daemon to run 'mpd'. Just remoce the package, and any other mpich* libmpich* stuff. Only openmpi should remain (openmpi openmpi-dev libopenmpi). Then, to make sure all is fine, try: sudo update-alternatives --config mpicc sudo update-alternatives --config mpirun Emmanuel. On 06/14/2012 01:49 PM, Jean-Francois.Moulin at hzg.de wrote: > Hi Emmanuel! > > thanks for the answer. Yes the build works but, this is what I get when I try to use it: > > (case A) > ~/Lab/MCarlo/McStas$ mcgui refsans_simplified_0.instr > ./refsans_simplified_0.out: error while loading shared libraries: libmpich.so.3: cannot open shared object file: No such file or directory > > And this is correct, the file is not on my system... why did the configure look for mpich in the first place? > > (caseB) > Well it wants MPICH? I tried and installed mpich2 from ubuntu repos (including dev), ./configure make make install... > mcgui now starts without problem and shows my instrument parameters (it did not in case A) > but the simulation returns errors... > > mcrun: No MPI/grid machine list. Running locally. > Define /home/jfmoulin/.mcstas/hosts > or /usr/local/lib/mcstas/tools/perl/hosts > or use option --machines= > [jfm-lap:11887] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 357 > [jfm-lap:11887] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 230 > [jfm-lap:11887] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../orte/runtime/orte_init.c at line 132 > -------------------------------------------------------------------------- > It looks like orte_init failed for some reason; your parallel process is > likely to abort. There are many reasons that a parallel process can > fail during orte_init; some of which are due to configuration or > environment problems. This failure appears to be an internal failure; > here's some additional information (which may only be relevant to an > Open MPI developer): > > orte_ess_set_name failed > --> Returned value A system-required executable either could not be found or was not executable by this user (-127) instead of ORTE_SUCCESS > > > Is there a reason to have conflicts between the two mpi (I have dependencies of other packages on openmpi) or do I forget a setup step? > I had the box running before and did not change my home dir so I guess it should still work > Anyway, thanks for your help! > > Ciao > JF > - > Helmholtz Zentrum Geesthacht > Institut f?r Werkstoffforschung > Abteilung WPN, Instrument REFSANS > Lichtenbergstr. 1 > 85747 Garching FRM II > Tel.: +49 (0)89 289 10762 > Internet: http://www.frm2.tum.de > > -----Emmanuel FARHI schrieb: ----- > An: Jean-Francois.Moulin at hzg.de, "McStas users list at mcstas.org" > Von: Emmanuel FARHI > Datum: 06/14/2012 10:22AM > Betreff: Re: [mcstas-users] openmpi compilation problem > > Hi Jean-Francois, > > to my knowledge, this is just a warning. The tar.gz configure; make; > make install should proceed OK still, and McStas should be able to find > MPI if 'mpicc' and 'mpirun' commands are available at the prompt. > > OpenMPI seems OK on recent systems. It was less reliable than MPICH > until 2010-2011 (would stall for long simulations with e.g. ncount> 2e9). > > Emmanuel. > > On 06/13/2012 05:36 PM, Jean-Francois.Moulin at hzg.de wrote: >> Hi to all! >> >> new Linux distro, new problem! On Linux Mint 13 I do not manage to install due to mpi problems. As already suggested some months ago I installed openmpi (packages from Ubuntu repos: libopenmpi 1.4.3.2 and its dev). >> The ./configure tells me that : >> checking mpi.h presence... no >> checking for mpi.h... no >> WARNING: /usr/bin/mpicc may fail to compile without mpi.h >> >> but I find this on my system: >> ./usr/lib/openmpi/include/mpi.h >> After reading the output of configure -h, I tried >> ./configure -I/usr/lib/openmpi/include/: >> configure: error: unrecognized option: `-I' >> I tried putting this path in the cppflags envirt variable. To no avail. >> seems I miss the point. >> Since I get a Makefile I looked for an include section where I could manually put the path but that does not look so easy... (for me) >> >> second question I am on a 64 bit machine, I should thus configure --with-pic right? >> >> Thanks in advance for your help! >> >> Best >> >> Jean-Francois >> >> >> - >> Helmholtz Zentrum Geesthacht >> Institut f?r Werkstoffforschung >> Abteilung WPN, Instrument REFSANS >> Lichtenbergstr. 1 >> 85747 Garching FRM II >> Tel.: +49 (0)89 289 10762 >> Internet: http://www.frm2.tum.deHelmholtz-Zentrum Geesthacht >> Zentrum f?r Material- und K?stenforschung GmbH >> Max-Planck-Stra?e 1 I 21502 Geesthacht I Deutschland/Germany >> >> Gesch?ftsf?hrer/Board of Management: Prof. Dr. Wolfgang Kaysser, Dipl.-Ing. Michael Gan? >> Vorsitzender des Aufsichtsrates/Chairman of the Supervisory Board: MinDirig Wilfried Kraus >> Amtsgericht L?beck HRB 285 GE (Register Court) >> Internet: http://www.hzg.de >> _______________________________________________ >> mcstas-users mailing list >> mcstas-users at mcstas.org >> http://mailman.mcstas.org/cgi-bin/mailman/listinfo/mcstas-users -- Emmanuel FARHI,www.ill.eu/computing/people/emmanuel-farhi \|/ ____ \|/ CS-Group ILL4/221, Institut Laue-Langevin (ILL) Grenoble ~@-/ oO \-@~ 6 rue J. Horowitz, BP 156, 38042 Grenoble Cedex 9,France /_( \__/ )_\ Work :Tel (33/0) 4 76 20 71 35. Fax (33/0) 4 76 48 39 06 \__U_/ From Jean-Francois.Moulin at hzg.de Fri Jun 15 13:24:34 2012 From: Jean-Francois.Moulin at hzg.de (Jean-Francois.Moulin at hzg.de) Date: Fri, 15 Jun 2012 13:24:34 +0200 Subject: [mcstas-users] openmpi compilation problem In-Reply-To: <4FDA09A8.1020605@ill.eu> References: <4FDA09A8.1020605@ill.eu>, <4FD99DA0.1040909@ill.eu>, Message-ID: Hi Emmanuel and Peter! thanks for the answers! I did a fresh install of openmpi after removing mpich2. I had to give the config...perl the location of the mpicc (mpirun was there already) Runs without trouble. I am now trying to install openvrml which apparently depends on a libjs which is not in repos... any better alternative ? (there seems to be a way out which probably will require some google work, I will try that asap). Best and thanks again, have a nice we (Sun is shining on this side of the Alps ;0) JF - Helmholtz Zentrum Geesthacht Institut f?r Werkstoffforschung Abteilung WPN, Instrument REFSANS Lichtenbergstr. 1 85747 Garching FRM II Tel.: +49 (0)89 289 10762 Internet: http://www.frm2.tum.de -----mcstas-users-bounces at mcstas.org schrieb: ----- An: mcstas-users at mcstas.org Von: Emmanuel FARHI Gesendet von: mcstas-users-bounces at mcstas.org Datum: 06/14/2012 06:03PM Betreff: Re: [mcstas-users] openmpi compilation problem Yes, you probably have conflicts between the two MPI packages. I would recommend to suppress MPICH2, which requires a daemon to run 'mpd'. Just remoce the package, and any other mpich* libmpich* stuff. Only openmpi should remain (openmpi openmpi-dev libopenmpi). Then, to make sure all is fine, try: sudo update-alternatives --config mpicc sudo update-alternatives --config mpirun Emmanuel. On 06/14/2012 01:49 PM, Jean-Francois.Moulin at hzg.de wrote: > ? Hi Emmanuel! > > thanks for the answer. Yes the build works but, this is what I get when I try to use it: > > (case A) > ~/Lab/MCarlo/McStas$ mcgui refsans_simplified_0.instr > ./refsans_simplified_0.out: error while loading shared libraries: libmpich.so.3: cannot open shared object file: No such file or directory > > And this is correct, the file is not on my system... why did the configure look for mpich in the first place? > > (caseB) > Well it wants MPICH? I tried and installed mpich2 from ubuntu repos (including dev), ./configure make make install... > mcgui now starts without problem and shows my instrument parameters (it did not in case A) > but the simulation returns errors... > > mcrun: No MPI/grid machine list. Running locally. > ? ?Define /home/jfmoulin/.mcstas/hosts > ? ?or /usr/local/lib/mcstas/tools/perl/hosts > ? ?or use option --machines= > [jfm-lap:11887] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 357 > [jfm-lap:11887] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 230 > [jfm-lap:11887] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../orte/runtime/orte_init.c at line 132 > -------------------------------------------------------------------------- > It looks like orte_init failed for some reason; your parallel process is > likely to abort. ?There are many reasons that a parallel process can > fail during orte_init; some of which are due to configuration or > environment problems. ?This failure appears to be an internal failure; > here's some additional information (which may only be relevant to an > Open MPI developer): > > ? ?orte_ess_set_name failed > ? ?--> ?Returned value A system-required executable either could not be found or was not executable by this user (-127) instead of ORTE_SUCCESS > > > Is there a reason to have conflicts between the two mpi (I have dependencies of other packages on openmpi) or do I forget a setup step? > I had the box running before and did not change my home dir so I guess it should still work > Anyway, thanks for your help! > > Ciao > JF > - > Helmholtz Zentrum Geesthacht > Institut f?r Werkstoffforschung > Abteilung WPN, Instrument REFSANS > Lichtenbergstr. 1 > 85747 Garching FRM II > Tel.: +49 (0)89 289 10762 > Internet: http://www.frm2.tum.de > > -----Emmanuel FARHI ?schrieb: ----- > An: Jean-Francois.Moulin at hzg.de, "McStas users list at mcstas.org" > Von: Emmanuel FARHI > Datum: 06/14/2012 10:22AM > Betreff: Re: [mcstas-users] openmpi compilation problem > > Hi Jean-Francois, > > to my knowledge, this is just a warning. The tar.gz configure; make; > make install should proceed OK still, and McStas should be able to find > MPI if 'mpicc' and 'mpirun' commands are available at the prompt. > > OpenMPI seems OK on recent systems. It was less reliable than MPICH > until 2010-2011 (would stall for long simulations with e.g. ncount> ?2e9). > > Emmanuel. > > On 06/13/2012 05:36 PM, Jean-Francois.Moulin at hzg.de wrote: >> Hi to all! >> >> new Linux distro, new problem! On Linux Mint 13 I do not manage to install due to mpi problems. As already suggested some months ago I installed openmpi (packages from Ubuntu repos: libopenmpi 1.4.3.2 and its dev). >> The ./configure tells me that : >> checking mpi.h presence... no >> checking for mpi.h... no >> WARNING: /usr/bin/mpicc may fail to compile without mpi.h >> >> but I find this on my system: >> ./usr/lib/openmpi/include/mpi.h >> After reading the output of configure -h, I tried >> ? ?./configure -I/usr/lib/openmpi/include/: >> configure: error: unrecognized option: `-I' >> I tried putting this path in the cppflags envirt variable. To no avail. >> seems I miss the point. >> Since I get a Makefile I looked for an include section where I could manually put the path but that does not look so easy... (for me) >> >> second question I am on a 64 bit machine, I should thus configure --with-pic right? >> >> Thanks in advance for your help! >> >> Best >> >> Jean-Francois >> >> >> - >> Helmholtz Zentrum Geesthacht >> Institut f?r Werkstoffforschung >> Abteilung WPN, Instrument REFSANS >> Lichtenbergstr. 1 >> 85747 Garching FRM II >> Tel.: +49 (0)89 289 10762 >> Internet: http://www.frm2.tum.deHelmholtz-Zentrum?Geesthacht >> Zentrum f?r Material- und K?stenforschung GmbH >> Max-Planck-Stra?e 1 I 21502 Geesthacht I Deutschland/Germany >> >> Gesch?ftsf?hrer/Board of Management: Prof. Dr. Wolfgang Kaysser, Dipl.-Ing. Michael Gan? >> Vorsitzender des Aufsichtsrates/Chairman of the Supervisory Board: MinDirig Wilfried Kraus >> Amtsgericht L?beck HRB 285 GE (Register Court) >> Internet: http://www.hzg.de >> _______________________________________________ >> mcstas-users mailing list >> mcstas-users at mcstas.org >> http://mailman.mcstas.org/cgi-bin/mailman/listinfo/mcstas-users -- Emmanuel FARHI,www.ill.eu/computing/people/emmanuel-farhi \|/ ____ \|/ CS-Group ILL4/221, Institut Laue-Langevin (ILL) Grenoble ?~@-/ oO \-@~ 6 rue J. Horowitz, BP 156, 38042 Grenoble Cedex 9,France ?/_( \__/ )_\ Work :Tel (33/0) 4 76 20 71 35. Fax (33/0) 4 76 48 39 06 ? ? \__U_/ _______________________________________________ mcstas-users mailing list mcstas-users at mcstas.org http://mailman.mcstas.org/cgi-bin/mailman/listinfo/mcstas-users Helmholtz-Zentrum Geesthacht Zentrum f?r Material- und K?stenforschung GmbH Max-Planck-Stra?e 1 I 21502 Geesthacht I Deutschland/Germany Gesch?ftsf?hrer/Board of Management: Prof. Dr. Wolfgang Kaysser, Dipl.-Ing. Michael Gan? Vorsitzender des Aufsichtsrates/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Amtsgericht L?beck HRB 285 GE (Register Court) Internet: http://www.hzg.de From pkwi at fysik.dtu.dk Fri Jun 15 13:37:38 2012 From: pkwi at fysik.dtu.dk (=?iso-8859-1?Q?Peter_Kj=E6r_Willendrup?=) Date: Fri, 15 Jun 2012 13:37:38 +0200 Subject: [mcstas-users] openmpi compilation problem In-Reply-To: References: <4FDA09A8.1020605@ill.eu>, <4FD99DA0.1040909@ill.eu>, Message-ID: <29DEAB6C-4CF2-425E-B391-B617D88D97B8@fysik.dtu.dk> Hi Jean-Francois, Good that you found a solution! For a VRML browser I tend to prefer FreeWRL - see http://freewrl.sourceforge.net/install_LinuxRelease.html for a Debian package repository. The Whitedune package (which is likely in Linux Mint) is also OK. Best, Peter On Jun 15, 2012, at 13:24 , > wrote: Hi Emmanuel and Peter! thanks for the answers! I did a fresh install of openmpi after removing mpich2. I had to give the config...perl the location of the mpicc (mpirun was there already) Runs without trouble. I am now trying to install openvrml which apparently depends on a libjs which is not in repos... any better alternative ? (there seems to be a way out which probably will require some google work, I will try that asap). Best and thanks again, have a nice we (Sun is shining on this side of the Alps ;0) JF - Helmholtz Zentrum Geesthacht Institut f?r Werkstoffforschung Abteilung WPN, Instrument REFSANS Peter Kj?r Willendrup Development engineer DTU Physics Technical University of Denmark [cid:image002.gif at 01CCCAF1.5E6331F0] Department of Physics Fysikvej Building 307 DK-2800 Kongens Lyngby Direct +45 2125 4612 Mobil +45 2125 4612 Fax +45 4593 2399 pkwi at fysik.dtu.dk -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.gif Type: image/gif Size: 58 bytes Desc: image001.gif URL: -------------- next part -------------- A non-text attachment was scrubbed... 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