Additional comment: on some shells "setenv" command should be used instead of "export": setenv P4_GLOBMEMSIZE 50000000
to be sure that the variable is really set type "export" or "setenv" without parameters and find P4_GLOBMEMSIZE in the list. On 31/05/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
Mariusz, I don't know how your machine is set up, but it seems at least from the message you get, it didn't work with .bash_profile. Maybe you try it as Yurko suggests: > you're quite right. I also have had this issue for big cells. just try >export P4_GLOBMEMSIZE=50000000 >or smth like this, before running siesta - it should work. Heribert Original Message: ----------------- From: Mariusz Krawiec [EMAIL PROTECTED] Date: Thu, 31 May 2007 14:00:37 +0200 To: [email protected] Subject: Re: [SIESTA-L] parallel mode problem Dear Heribert, Of course. I put it into ma .bash_profile file to have it on all nodes. It didn't help. Do you think I should do this before compilation of siesta or just before running? All the best, Mariusz. ---------------------------------------------------------------------- Dr Mariusz Krawiec Institute of Physics Phone: +48 81 537 6146 M Curie-Sklodowska University Fax: +48 81 537 6191 pl. M. Curie-Sklodowskiej 1 E-mail: [EMAIL PROTECTED] 20-031 Lublin, Poland http://www.fnano.umcs.lublin.pl ---- ---- If you think of MS-DOS as mono, and Windows as stereo, then Linux is Dolby Pro-Logic Surround Sound with Bass Boost and all the music is free. - unknown ---- ---- On Thu, 31 May 2007, [EMAIL PROTECTED] wrote: > Dear Mariusz, > > Did you try what the error message suggests? > > InitMesh: Mesh cutoff (required, used) = 225.000 244.755 Ry > p0_5146: (60.036989) xx_shmalloc: returning NULL; requested 4976688 bytes > p0_5146: (60.036989) p4_shmalloc returning NULL; request = 4976688 bytes > => You can increase the amount of memory by setting the environment variable > => P4_GLOBMEMSIZE (in bytes); the current size is 4194304 > > Cheers, > Heribert Reis > > ---------------------------------------------------------------------- > Dr Mariusz Krawiec > Institute of Physics Phone: +48 81 537 6146 > M Curie-Sklodowska University Fax: +48 81 537 6191 > pl. M. Curie-Sklodowskiej 1 E-mail: [EMAIL PROTECTED] > 20-031 Lublin, Poland http://www.fnano.umcs.lublin.pl > > ---- ---- > If you think of MS-DOS as mono, and Windows as stereo, then Linux is > Dolby Pro-Logic Surround Sound with Bass Boost and all the music is > free. - unknown > ---- ---- > > On Wed, 30 May 2007, Marcos Verissimo Alves wrote: > >> Hi Mariusz, >> >> I would use O2 optimization instead of O3. O3 does not always yield >> improvements in performance, and can in some cases lead to numerical >> errors. However, from your error messages, I would guess the error could >> lie not in siesta, but in the mpi compilation - that is, if mpi is >> compiled from scratch. Just a wild guess. >> >> Cheers, >> >> Marcos >> >>> Dear Siesta users, >>> >>> Happy to join the list. >>> >>> I have a problem with running Siesta in parallel mode on IA64 cluster. >>> >>> The compilation was sucessful, albeit with some warnings: >>> >>> fortcom: Warning: Optimization suppressed due to excessive resource >>> requirements; contact Intel Premier Support >>> in file siesta.F, line 11, column 0 >>> >>> At the end I got executable file. >>> For compilation (following arch.make file distributed with Siesta) I > used: >>> >>> ifort -Vaxlib -c -O3 -tpp2 -W0 -DMPI -DNODAT -DWXML_INIT_FIX >>> -DHAS_DLAMC3 -DALLOC_SAVE_BUG >>> >>> When I try to run it on 2 processors (mpirun -np 2) the program stops and >>> I get a message: >>> >>> rm_5015: p4_error: semget failed for setnum: 0 >>> p0_16457: (0.200573) net_recv failed for fd = 5 >>> p0_16457: p4_error: net_recv read, errno = : 104 >>> >>> When I run on one processor only (mpirun -np 1) everything is ok. >>> Note that siesta is compiled to run in parallel mode. >>> >>> Thanks for any suggestions. >>> Mariusz. >>> >>> >>> ---------------------------------------------------------------------- >>> Dr Mariusz Krawiec >>> Institute of Physics Phone: +48 81 537 6146 >>> M Curie-Sklodowska University Fax: +48 81 537 6191 >>> pl. M. Curie-Sklodowskiej 1 E-mail: [EMAIL PROTECTED] >>> 20-031 Lublin, Poland http://www.fnano.umcs.lublin.pl >>> >>> ---- ---- >>> If you think of MS-DOS as mono, and Windows as stereo, then Linux is >>> Dolby Pro-Logic Surround Sound with Bass Boost and all the music is >>> free. - unknown >>> ---- ---- >>> >> >> >> -- >> Dr. Marcos Verissimo Alves >> Post-Doctoral Fellow >> Condensed Matter and Statistical Physics Sector >> International Centre for Theoretical Physics >> Trieste, Italy >> >> -------- >> >> I have become so addicted to vi that I try to exit OpenOffice by typing > :wq! >> > > -------------------------------------------------------------------- > mail2web - Check your email from the web at > http://link.mail2web.com/mail2web > -------------------------------------------------------------------- mail2web.com – What can On Demand Business Solutions do for you? http://link.mail2web.com/Business/SharePoint
-- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED]
