[Wien] error setrlimit(): Invalid argument
Dear Wien2k users, I am now facing a new but related error to the previous one: Now the error says: setrlimit(): Invalid argument stop error My OS: Cluster, PBS Pro (SGI ProPack6SP2 AltixXE 250 2CPU/8core 32GB Memory), Suse Enterprise Server 10 (x86-64), I am using ssh login. After I have the supercell struct file in place and init_lapw, in the working directory I do run_lapw -p -ec 0.0001 - then instantly I got the above mentioned error, the lapw does not seem to start running at all. A ls -l *.error gives four error files but all of them are of size of zero. Originally I traced the similar error to the Stack size setting problem, and with Professor Marks' help I had commented out the line ulimit -s unlimit out from my .bashrc file, and I have logout the cluster and relogin more than twice. I search the email achieve without result, I googled it but it points to me the same place as I previously had (Stack Size setting issue - but that is no an issue at lest in the .bashrc file anymore) - Now I don't know where to go from here. Any help/hint would be much appreciated. Thank you very much. Kind regards, Qiwen === --Original Message-- From:Laurence MarksL-marks at northwestern.edu To:A Mailing list for WIEN2k userswien at zeus.theochem.tuwien.ac.at Cc: Subject:Re: [Wien] commenting out the line ulimit -s unlimit from .bashrc? Date:07/29/2011 06:14:14 AM(-0500) Delete the line -- if he has already set it as unlimited. On Fri, Jul 29, 2011 at 5:19 AM, Dr Qiwen YAO Yao.Qiwen at nims.go.jp wrote: Dear Wien2k users, I've come across an issue when running WIEN2k 11 in a cluster (PBS Pro, SUSE Linux Enterprise Server 10 (x86_64)) for the Stack size setting permission: It was the system policy that a user is not allowed to set the stack size in anyway. ?That is: ulimit -s whateveramount is not allowed - so for the line inserted in my .bashrc file by WIEN, how do I go around this problem? The system support is not changing anything for this in his side (but he said that the stack size is unlimited on computer nodes when users run jobs). So can I just delete this line from the .bashrc file? Would that affect the WIEN2k execution? Thank you, Qiwen Yao ** Dr QiWen YAO JSPS Fellow Multifunctional Materials Group Optical and Electronic Materials Unit Environment and Energy Materials Research Division National Institute for Materials Science 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan Phone: +81-29-851-3354, ext. no. 6482, Fax: +81-29-859-2501 ** ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- Laurence Marks Department of Materials Science and Engineering MSE Rm 2036 Cook Hall 2220 N Campus Drive Northwestern University Evanston, IL 60208, USA Tel: (847) 491-3996 Fax: (847) 491-7820 email: L-marks at northwestern dot edu Web: www.numis.northwestern.edu Chair, Commission on Electron Crystallography of IUCR www.numis.northwestern.edu/ Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ** Dr QiWen YAO JSPS Fellow Multifunctional Materials Group Optical and Electronic Materials Unit Environment and Energy Materials Research Division National Institute for Materials Science 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan Phone: +81-29-851-3354, ext. no. 6482, Fax: +81-29-859-2501 **
[Wien] error setrlimit(): Invalid argument
Dear Professor Marks, The file W2kutils.h you sent is identical to the ones in these three directories - they are with the exact same size and I have also checked line by line - no difference found. Both of these original files in my installed WIEN are the same as the corresponding ones at the Wien2k site - I have also checked that. The file W2kutils.c you sent is newer (last changed date Aug 2010) compared to the ones I have in the three directories (time-stamp: Jan 2010). So I replaced this file in the SRC_lapw0 directory and recompiled the WIEN2k, and run x lapw0 -p successfully - see below: a010220 at asahi01:/data1/a010220/wiendata/SrNdCoO4 x lapw0 -p starting parallel lapw0 at Sat Jul 30 02:29:08 JST 2011 .machine0 : processors running lapw0 in single mode LAPW0 END 293.950u 11.848s 5:07.46 99.4% 0+0k 0+0io 252pf+0w So it seems that you've solve the problem! Should i also do the same to the file W2kutils.c for the other two (SRC_lap1,2) directories and recompile the WIEN and then run the parallel job ? Thank you so much for your time and help. Kind regards, Qiwen --Original Message-- From:Laurence MarksL-marks at northwestern.edu To:A Mailing list for WIEN2k userswien at zeus.theochem.tuwien.ac.at Cc: Subject:Re: [Wien] error setrlimit(): Invalid argument Date:07/29/2011 10:24:49 AM(-0500) Please check your version of the two attached files against what you have in SRC_lapw0,1,2 . (I think the attached is the latest version, but please also check the Wien2k site, just one of SRC_lapw0.) If they are different, copy what you have somewhere then replace them in SRC_lapw0 (as a test), recompile and just run x lapw0 -p. This may be one of many things, but it is related to these files: a) Your C compiler is strange (which did you use, icc or gcc?) b) Your sysadmin has prevented you as a user from making the call At worst, comment out the w2k_extend_limits() subroutine. Maybe your sysadmin can help work out what is appropriate for your system -- unfortunately C is not as standard as fortran. (We can then patch around this in the future.) Quick explanation. If you look back in the mailing list, you will find about once a week, an error/email associated with ulimit. This got worse with openmpi since in this code there is no way to set the stacksize. This subroutine does it for you, but is not working on your system for some reason. There was a similar bug on a Mac which I believe is cured with this version. On Fri, Jul 29, 2011 at 9:23 AM, Dr Qiwen YAO Yao.Qiwen at nims.go.jp wrote: Dear Wien2k users, I am now facing a new but related error to the previous one: Now the error says: setrlimit(): Invalid argument ? stop error My OS: Cluster, PBS Pro (SGI ProPack6SP2 AltixXE 250 2CPU/8core 32GB Memory), Suse Enterprise Server 10 (x86-64), I am using ssh login. After I have the supercell struct file in place and init_lapw, in the working directory I do run_lapw -p -ec 0.0001 ?- then instantly I got the above mentioned error, the lapw does not seem to start running at all. A ls -l *.error gives four error files but all of them are of size of zero. Originally I traced the similar error to the Stack size setting problem, and with Professor Marks' help I had commented out the line ulimit -s unlimit out from my .bashrc file, and I have logout the cluster and relogin more than twice. I search the email achieve without result, I googled it but it points to me the same place as I previously had (Stack Size setting issue - but that is no an issue at lest in the .bashrc file anymore) - Now I don't know where to go from here. Any help/hint would be much appreciated. Thank you very much. Kind regards, Qiwen === --Original Message-- From:Laurence MarksL-marks at northwestern.edu To:A Mailing list for WIEN2k userswien at zeus.theochem.tuwien.ac.at Cc: Subject:Re: [Wien] commenting out the line ulimit -s unlimit from .bashrc? Date:07/29/2011 06:14:14 AM(-0500) Delete the line -- if he has already set it as unlimited. On Fri, Jul 29, 2011 at 5:19 AM, Dr Qiwen ?YAO Yao.Qiwen at nims.go.jp wrote: Dear Wien2k users, I've come across an issue when running WIEN2k 11 in a cluster (PBS Pro, SUSE Linux Enterprise Server 10 (x86_64)) for the Stack size setting permission: It was the system policy that a user is not allowed to set the stack size in anyway. ?That is: ulimit -s whateveramount is not allowed - so for the line inserted in my .bashrc file by WIEN, how do I go around this problem? The system support is not changing anything for this in his side (but he said that the stack size is unlimited on computer nodes when users run jobs). So can I just delete this line from the .bashrc file? Would that affect the WIEN2k execution? Thank you, Qiwen Yao ** Dr QiWen YAO JSPS Fellow Multifunctional Materials Group Optical
[Wien] error setrlimit(): Invalid argument
Dear Professor Marks, Thank you so much for your kind help and your time Kind regards, Qiwen --Original Message-- From:Laurence MarksL-marks at northwestern.edu To:A Mailing list for WIEN2k userswien at zeus.theochem.tuwien.ac.at Cc: Subject:Re: [Wien] error setrlimit(): Invalid argument Date:07/29/2011 01:01:50 PM(-0500) Yes, and anywhere else (mixer, perhaps some others ) -- do ls */W2kutils.c N.B., of course you only need to recompile the relevant directories. On Fri, Jul 29, 2011 at 12:51 PM, Dr Qiwen YAO Yao.Qiwen at nims.go.jp wrote: Dear Professor Marks, The file W2kutils.h you sent is identical to the ones in these three directories - they are with the exact same size and I have also checked line by line - no difference found. Both of these original files in my installed WIEN are the same as the corresponding ones at the Wien2k site - I have also checked that. The file W2kutils.c you sent is newer (last changed date Aug 2010) compared to the ones I have in the three directories (time-stamp: Jan 2010). So I replaced this file in the SRC_lapw0 directory and recompiled the WIEN2k, and run x lapw0 -p successfully - see below: a010220 at asahi01:/data1/a010220/wiendata/SrNdCoO4 x lapw0 -p starting parallel lapw0 at Sat Jul 30 02:29:08 JST 2011 .machine0 : processors running lapw0 in single mode ?LAPW0 END 293.950u 11.848s 5:07.46 99.4% 0+0k 0+0io 252pf+0w So it seems that you've solve the problem! Should i also do the same to the file W2kutils.c for the other two (SRC_lap1,2) directories and recompile the WIEN and then run the parallel job ? Thank you so much for your time and help. Kind regards, Qiwen --Original Message-- From:Laurence MarksL-marks at northwestern.edu To:A Mailing list for WIEN2k userswien at zeus.theochem.tuwien.ac.at Cc: Subject:Re: [Wien] error setrlimit(): Invalid argument Date:07/29/2011 10:24:49 AM(-0500) Please check your version of the two attached files against what you have in SRC_lapw0,1,2 . (I think the attached is the latest version, but please also check the Wien2k site, just one of SRC_lapw0.) If they are different, copy what you have somewhere then replace them in SRC_lapw0 (as a test), recompile and just run x lapw0 -p. This may be one of many things, but it is related to these files: a) Your C compiler is strange (which did you use, icc or gcc?) b) Your sysadmin has prevented you as a user from making the call At worst, comment out the w2k_extend_limits() subroutine. Maybe your sysadmin can help work out what is appropriate for your system -- unfortunately C is not as standard as fortran. (We can then patch around this in the future.) Quick explanation. If you look back in the mailing list, you will find about once a week, an error/email associated with ulimit. This got worse with openmpi since in this code there is no way to set the stacksize. This subroutine does it for you, but is not working on your system for some reason. There was a similar bug on a Mac which I believe is cured with this version. On Fri, Jul 29, 2011 at 9:23 AM, Dr Qiwen ?YAO Yao.Qiwen at nims.go.jp wrote: Dear Wien2k users, I am now facing a new but related error to the previous one: Now the error says: setrlimit(): Invalid argument ? stop error My OS: Cluster, PBS Pro (SGI ProPack6SP2 AltixXE 250 2CPU/8core 32GB Memory), Suse Enterprise Server 10 (x86-64), I am using ssh login. After I have the supercell struct file in place and init_lapw, in the working directory I do run_lapw -p -ec 0.0001 ?- then instantly I got the above mentioned error, the lapw does not seem to start running at all. A ls -l *.error gives four error files but all of them are of size of zero. Originally I traced the similar error to the Stack size setting problem, and with Professor Marks' help I had commented out the line ulimit -s unlimit out from my .bashrc file, and I have logout the cluster and relogin more than twice. I search the email achieve without result, I googled it but it points to me the same place as I previously had (Stack Size setting issue - but that is no an issue at lest in the .bashrc file anymore) - Now I don't know where to go from here. Any help/hint would be much appreciated. Thank you very much. Kind regards, Qiwen === --Original Message-- From:Laurence MarksL-marks at northwestern.edu To:A Mailing list for WIEN2k userswien at zeus.theochem.tuwien.ac.at Cc: Subject:Re: [Wien] commenting out the line ulimit -s unlimit from .bashrc? Date:07/29/2011 06:14:14 AM(-0500) Delete the line -- if he has already set it as unlimited. On Fri, Jul 29, 2011 at 5:19 AM, Dr Qiwen ?YAO Yao.Qiwen at nims.go.jp wrote: Dear Wien2k users, I've come across an issue when running WIEN2k 11 in a cluster (PBS Pro, SUSE Linux Enterprise Server 10 (x86_64)) for the Stack size setting permission: It was the system policy that a user
[Wien] error setrlimit(): Invalid argument
Please check your version of the two attached files against what you have in SRC_lapw0,1,2 . (I think the attached is the latest version, but please also check the Wien2k site, just one of SRC_lapw0.) If they are different, copy what you have somewhere then replace them in SRC_lapw0 (as a test), recompile and just run x lapw0 -p. This may be one of many things, but it is related to these files: a) Your C compiler is strange (which did you use, icc or gcc?) b) Your sysadmin has prevented you as a user from making the call At worst, comment out the w2k_extend_limits() subroutine. Maybe your sysadmin can help work out what is appropriate for your system -- unfortunately C is not as standard as fortran. (We can then patch around this in the future.) Quick explanation. If you look back in the mailing list, you will find about once a week, an error/email associated with ulimit. This got worse with openmpi since in this code there is no way to set the stacksize. This subroutine does it for you, but is not working on your system for some reason. There was a similar bug on a Mac which I believe is cured with this version. On Fri, Jul 29, 2011 at 9:23 AM, Dr Qiwen YAO Yao.Qiwen at nims.go.jp wrote: Dear Wien2k users, I am now facing a new but related error to the previous one: Now the error says: setrlimit(): Invalid argument ? stop error My OS: Cluster, PBS Pro (SGI ProPack6SP2 AltixXE 250 2CPU/8core 32GB Memory), Suse Enterprise Server 10 (x86-64), I am using ssh login. After I have the supercell struct file in place and init_lapw, in the working directory I do run_lapw -p -ec 0.0001 ?- then instantly I got the above mentioned error, the lapw does not seem to start running at all. A ls -l *.error gives four error files but all of them are of size of zero. Originally I traced the similar error to the Stack size setting problem, and with Professor Marks' help I had commented out the line ulimit -s unlimit out from my .bashrc file, and I have logout the cluster and relogin more than twice. I search the email achieve without result, I googled it but it points to me the same place as I previously had (Stack Size setting issue - but that is no an issue at lest in the .bashrc file anymore) - Now I don't know where to go from here. Any help/hint would be much appreciated. Thank you very much. Kind regards, Qiwen === --Original Message-- From:Laurence MarksL-marks at northwestern.edu To:A Mailing list for WIEN2k userswien at zeus.theochem.tuwien.ac.at Cc: Subject:Re: [Wien] commenting out the line ulimit -s unlimit from .bashrc? Date:07/29/2011 06:14:14 AM(-0500) Delete the line -- if he has already set it as unlimited. On Fri, Jul 29, 2011 at 5:19 AM, Dr Qiwen ?YAO Yao.Qiwen at nims.go.jp wrote: Dear Wien2k users, I've come across an issue when running WIEN2k 11 in a cluster (PBS Pro, SUSE Linux Enterprise Server 10 (x86_64)) for the Stack size setting permission: It was the system policy that a user is not allowed to set the stack size in anyway. ?That is: ulimit -s whateveramount is not allowed - so for the line inserted in my .bashrc file by WIEN, how do I go around this problem? The system support is not changing anything for this in his side (but he said that the stack size is unlimited on computer nodes when users run jobs). So can I just delete this line from the .bashrc file? Would that affect the WIEN2k execution? Thank you, Qiwen Yao ** Dr QiWen YAO JSPS Fellow Multifunctional Materials Group Optical and Electronic Materials Unit Environment and Energy Materials Research Division National Institute for Materials Science 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan Phone: +81-29-851-3354, ext. no. 6482, Fax: +81-29-859-2501 ** ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- Laurence Marks Department of Materials Science and Engineering MSE Rm 2036 Cook Hall 2220 N Campus Drive Northwestern University Evanston, IL 60208, USA Tel: (847) 491-3996 Fax: (847) 491-7820 email: L-marks at northwestern dot edu Web: www.numis.northwestern.edu Chair, Commission on Electron Crystallography of IUCR www.numis.northwestern.edu/ Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ** Dr QiWen YAO JSPS Fellow Multifunctional Materials Group Optical and Electronic Materials Unit Environment and Energy Materials Research Division National Institute for Materials Science 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047,
[Wien] error setrlimit(): Invalid argument
Yes, and anywhere else (mixer, perhaps some others ) -- do ls */W2kutils.c N.B., of course you only need to recompile the relevant directories. On Fri, Jul 29, 2011 at 12:51 PM, Dr Qiwen YAO Yao.Qiwen at nims.go.jp wrote: Dear Professor Marks, The file W2kutils.h you sent is identical to the ones in these three directories - they are with the exact same size and I have also checked line by line - no difference found. Both of these original files in my installed WIEN are the same as the corresponding ones at the Wien2k site - I have also checked that. The file W2kutils.c you sent is newer (last changed date Aug 2010) compared to the ones I have in the three directories (time-stamp: Jan 2010). So I replaced this file in the SRC_lapw0 directory and recompiled the WIEN2k, and run x lapw0 -p successfully - see below: a010220 at asahi01:/data1/a010220/wiendata/SrNdCoO4 x lapw0 -p starting parallel lapw0 at Sat Jul 30 02:29:08 JST 2011 .machine0 : processors running lapw0 in single mode ?LAPW0 END 293.950u 11.848s 5:07.46 99.4% 0+0k 0+0io 252pf+0w So it seems that you've solve the problem! Should i also do the same to the file W2kutils.c for the other two (SRC_lap1,2) directories and recompile the WIEN and then run the parallel job ? Thank you so much for your time and help. Kind regards, Qiwen --Original Message-- From:Laurence MarksL-marks at northwestern.edu To:A Mailing list for WIEN2k userswien at zeus.theochem.tuwien.ac.at Cc: Subject:Re: [Wien] error setrlimit(): Invalid argument Date:07/29/2011 10:24:49 AM(-0500) Please check your version of the two attached files against what you have in SRC_lapw0,1,2 . (I think the attached is the latest version, but please also check the Wien2k site, just one of SRC_lapw0.) If they are different, copy what you have somewhere then replace them in SRC_lapw0 (as a test), recompile and just run x lapw0 -p. This may be one of many things, but it is related to these files: a) Your C compiler is strange (which did you use, icc or gcc?) b) Your sysadmin has prevented you as a user from making the call At worst, comment out the w2k_extend_limits() subroutine. Maybe your sysadmin can help work out what is appropriate for your system -- unfortunately C is not as standard as fortran. (We can then patch around this in the future.) Quick explanation. If you look back in the mailing list, you will find about once a week, an error/email associated with ulimit. This got worse with openmpi since in this code there is no way to set the stacksize. This subroutine does it for you, but is not working on your system for some reason. There was a similar bug on a Mac which I believe is cured with this version. On Fri, Jul 29, 2011 at 9:23 AM, Dr Qiwen ?YAO Yao.Qiwen at nims.go.jp wrote: Dear Wien2k users, I am now facing a new but related error to the previous one: Now the error says: setrlimit(): Invalid argument ? stop error My OS: Cluster, PBS Pro (SGI ProPack6SP2 AltixXE 250 2CPU/8core 32GB Memory), Suse Enterprise Server 10 (x86-64), I am using ssh login. After I have the supercell struct file in place and init_lapw, in the working directory I do run_lapw -p -ec 0.0001 ?- then instantly I got the above mentioned error, the lapw does not seem to start running at all. A ls -l *.error gives four error files but all of them are of size of zero. Originally I traced the similar error to the Stack size setting problem, and with Professor Marks' help I had commented out the line ulimit -s unlimit out from my .bashrc file, and I have logout the cluster and relogin more than twice. I search the email achieve without result, I googled it but it points to me the same place as I previously had (Stack Size setting issue - but that is no an issue at lest in the .bashrc file anymore) - Now I don't know where to go from here. Any help/hint would be much appreciated. Thank you very much. Kind regards, Qiwen === --Original Message-- From:Laurence MarksL-marks at northwestern.edu To:A Mailing list for WIEN2k userswien at zeus.theochem.tuwien.ac.at Cc: Subject:Re: [Wien] commenting out the line ulimit -s unlimit from .bashrc? Date:07/29/2011 06:14:14 AM(-0500) Delete the line -- if he has already set it as unlimited. On Fri, Jul 29, 2011 at 5:19 AM, Dr Qiwen ?YAO Yao.Qiwen at nims.go.jp wrote: Dear Wien2k users, I've come across an issue when running WIEN2k 11 in a cluster (PBS Pro, SUSE Linux Enterprise Server 10 (x86_64)) for the Stack size setting permission: It was the system policy that a user is not allowed to set the stack size in anyway. ?That is: ulimit -s whateveramount is not allowed - so for the line inserted in my .bashrc file by WIEN, how do I go around this problem? The system support is not changing anything for this in his side (but he said that the stack size is unlimited on computer nodes when users run
