[Pw_forum] ERROR IN: iotk_scan_dat_aux and iotk_scan_dat of IOTK LIBRARY?
Dear all QE users, i am getting errors in iotk while doing following tests: /tests$ ./check-pw.x.j Checking atom...passed Checking atom-lsda...passed Checking atom-pbe...discrepancy in pressure detected Reference: -14.44, You got: -14.43 Checking atom-sigmapbe...discrepancy in pressure detected Reference: -15.02, You got: -15.03 Checking berry...passed Checking berry, step 2 ... # FROM IOTK LIBRARY, VERSION 1.2.0 # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_scan_dat_aux (iotk_dat.spp:664) # CVS Revision: 1.27 # ERROR IN: iotk_scan_dat (iotk_dat.spp:740) # CVS Revision: 1.27 # Error reading data name=z.2 rkind=8 rlen=-1 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 FAILED with error condition! Input: berry.in2, Output: berry.out2, Reference: berry.ref2 Aborting I have this problem with Ubuntu OS, while i have no problem on Suse(SLED-11) and code works nicely there with same make.sys file. While executing "make all" command i got few warnings from iotk/src, which are : mpif90 -O2 -assume byterecl -g -traceback -nomodule -fpp -D__INTEL -D_SCALAPACK -D__FFTW3 -D__MPI -D__PARA -I../include -I/extra/sonu/intel/composerxe-2011.0.084/mkl/include/fftw -I/extra/sonu/mpich2-install/include -c iotk_base.f90 ../include/iotk_config.h(104): warning #5117: Bad # preprocessor line # 21 "iotk_base.spp" 2 --^ mpif90 -O2 -assume byterecl -g -traceback -nomodule -fpp -D__INTEL -D_SCALAPACK -D__FFTW3 -D__MPI -D__PARA -I../include -I/extra/sonu/intel/composerxe-2011.0.084/mkl/include/fftw -I/extra/sonu/mpich2-install/include -c iotk_attr_interf.f90 ../include/iotk_config.h(104): warning #5117: Bad # preprocessor line # 21 "iotk_attr_interf.spp" 2 -^ mpif90 -O2 -assume byterecl -g -traceback -nomodule -fpp -D__INTEL -D_SCALAPACK -D__FFTW3 -D__MPI -D__PARA -I../include -I/extra/sonu/intel/composerxe-2011.0.084/mkl/include/fftw -I/extra/sonu/mpich2-install/include -c iotk_error_interf.f90 ../include/iotk_config.h(104): warning #5117: Bad # preprocessor line # 21 "iotk_error_interf.spp" 2 --^ mpif90 -O2 -assume byterecl -g -traceback -nomodule -fpp -D__INTEL -D_SCALAPACK -D__FFTW3 -D__MPI -D__PARA -I../include -I/extra/sonu/intel/composerxe-2011.0.084/mkl/include/fftw -I/extra/sonu/mpich2-install/include -c iotk_attr+COMPLEX1_0.f90 iotk_attr.spp(221): remark #8291: Recommended relationship between field width 'W' and the number of fractional digits 'D' in this edit descriptor is 'W>=D+7'. read(string(pos+1:pos1-1),"(G100.95)",iostat=iostat) tmpreal -^ i think something to do with config.h file of iotk. I shall be thankful for any kind of help. with regards, Sonu Kumar Phd Student Physics Department Indian Institute of Technology Delhi-110016, India web:-http://www.iitd.ac.in/ -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101116/dac25eef/attachment-0001.htm
[Pw_forum] MPI_Bcast error from cp.x
Omololu Akin-Ojo wrote: > The program crashes (AIX) or writes the warning message (Linux) at the > point where it is supposed to print (iprint=X) "relevant physical > quantities to standard output ..." -- and very reproducible for any X. please provide a test P. -- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] MPI_Bcast error from cp.x
On Tue, Nov 16, 2010 at 4:38 PM, Paolo Giannozzi wrote: > > Omololu Akin-Ojo wrote: > > > It turns out that if one is NOT using orthogonalization='ortho' in > > optimizing the electrons, the eigenvalues should not be computed > > this is completely irrelevant I think this is important. It seems that the problem is caused by an attempt to calculate the eigenvalues and this attempt is triggered by "iprint." > > > My way of getting around it is to avoid printing "physical quantities to > > standard output" as it seems the error comes at the printing step. > > what makes you think that the error comes at the printing step? The program crashes (AIX) or writes the warning message (Linux) at the point where it is supposed to print (iprint=X) "relevant physical quantities to standard output ..." -- and very reproducible for any X. Grazie ancora. o. > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- * Seek GOD! *
[Pw_forum] MPI_Bcast error from cp.x
Omololu Akin-Ojo wrote: > It turns out that if one is NOT using orthogonalization='ortho' in > optimizing the electrons, the eigenvalues should not be computed this is completely irrelevant > My way of getting around it is to avoid printing "physical quantities to > standard output" as it seems the error comes at the printing step. what makes you think that the error comes at the printing step? P. -- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] MPI_Bcast error from cp.x
Omololu Akin-Ojo wrote: > I actually don't have a clue in which part of the program > I should increase/decrease buffer/message size. you shouldn't increase/decrease anything. You should look in the output file if there are other error messages. Then you should verify whether this error is reproducible ([referrably by running it on a different machine). If it is, please provide code version, input data, execution detail so that the error can be reproduced. If it is not: your compiler or MPI libraries are, with very high probability, buggy P. -- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] MPI_Bcast error from cp.x
Thanks, Paolo. It turns out that if one is NOT using orthogonalization='ortho' in optimizing the electrons, the eigenvalues should not be computed: NOTE: eigenvalues are not computed without ortho (I got this warning on a 64bit Linux while it crashes on AIX machine with the error I reported previously: ERROR: 0032-117 User pack or receive buffer is too small) My way of getting around it is to avoid printing "physical quantities to standard output" as it seems the error comes at the printing step. So, I set iprint (and isave) in the &control section to something larger than my maximum number of steps, nstep. It is still running so I don't know what it will do at the end. Grazie ancora. o. On Tue, Nov 16, 2010 at 7:19 AM, Paolo Giannozzi wrote: > Omololu Akin-Ojo wrote: > > > I actually don't have a clue in which part of the program > > I should increase/decrease buffer/message size. > > you shouldn't increase/decrease anything. You should look in the > output file if there are other error messages. Then you should > verify whether this error is reproducible ([referrably by running > it on a different machine). If it is, please provide code version, > input data, execution detail so that the error can be reproduced. > If it is not: your compiler or MPI libraries are, with very high > probability, buggy > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- * Seek GOD! * -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101116/95d7983a/attachment.htm
[Pw_forum] Help XSPectra calculation
Dear Suman Dhayal, fro; the output of your script it seems to me that you are not running at all the XSpectra example but the general QE example. And the segmentation fault that you find has little do to with xspectrq but this is connected with the bands.x file. The XSpectra examples are in another directory. M. >> >> >> > > -- > > Message: 8 > Date: Mon, 15 Nov 2010 23:58:25 -0600 > From: Suman Dhayal > Subject: [Pw_forum] Help! > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > hi, > > I configured and compiled the code but when I run example01, it runs for Si > but not for Al. It gives me a segmentation fault error and then says exit > status as follows: > > This example shows how to use pw.x to calculate the total energy and > the band structure of four simple systems: Si, Al, Cu, Ni. > > executables directory: /home/suman/Diff_folders/Diff_ > Codes/espresso-4.2.1/bin > pseudo directory: > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/espresso-4.2.1/pseudo > temporary directory: > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/Temp_data_file > checking that needed directories and files exist... done > > running pw.x as: > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/bin/pw.x > running bands.x as: > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/bin/bands.x > > cleaning > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/Temp_data_file... done > running the scf calculation for Si... done > running the band-structure calculation for Si... done > running the symmetry analysis for Si bands...Segmentation fault > done > cleaning > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/Temp_data_file... done > running the scf calculation for Al...Segmentation fault > Error condition encountered during test: exit status = 139 > Aborting > > Thanks for the help, > > Harli > -- next part -- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20101115/0b3385a5/attachment.htm > > > -- > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 41, Issue 28 > -- * * * * Matteo Calandra, Charge de Recherche (CR1) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 16, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra
[Pw_forum] Help XSPectra calculation
Dear Matteo, Thank you for the quick response. H, I want to run the XSpectra example which I did once but it did not run and aborted in between. So I went back to example01 as xspectra uses the output of 'pw.x' and 'gipaw.x'. So I got back to example01 and looked into the output files and I found that it's not run completely. The output files for Si are completely run but not for the Al, it stops in between only with the error message that I have posted here in the previous email. So the error message that I posted is from running example01 and not xspectra. And I have no idea, what may be wrong. So it would be very helpful if I could be guided a little over it. Thanks a lot, Harli On Tue, Nov 16, 2010 at 2:09 AM, Matteo Calandra < matteo.calandra at impmc.jussieu.fr> wrote: > Dear Suman Dhayal, > > fro; the output of your script it seems to me that you are not running > at all the XSpectra example but the general QE example. > And the segmentation fault that you find has little do to with xspectrq > but this is connected with the bands.x file. > > The XSpectra examples are in another directory. > > M. > > >> > >> > >> > > > > -- > > > > Message: 8 > > Date: Mon, 15 Nov 2010 23:58:25 -0600 > > From: Suman Dhayal > > Subject: [Pw_forum] Help! > > To: PWSCF Forum > > Message-ID: > >> mail.gmail.com > mail.gmail.com> > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > hi, > > > > I configured and compiled the code but when I run example01, it runs for > Si > > but not for Al. It gives me a segmentation fault error and then says exit > > status as follows: > > > > This example shows how to use pw.x to calculate the total energy and > > the band structure of four simple systems: Si, Al, Cu, Ni. > > > > executables directory: /home/suman/Diff_folders/Diff_ > > Codes/espresso-4.2.1/bin > > pseudo directory: > > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/espresso-4.2.1/pseudo > > temporary directory: > > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/Temp_data_file > > checking that needed directories and files exist... done > > > > running pw.x as: > > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/bin/pw.x > > running bands.x as: > > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/bin/bands.x > > > > cleaning > > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/Temp_data_file... done > > running the scf calculation for Si... done > > running the band-structure calculation for Si... done > > running the symmetry analysis for Si bands...Segmentation fault > > done > > cleaning > > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/Temp_data_file... done > > running the scf calculation for Al...Segmentation fault > > Error condition encountered during test: exit status = 139 > > Aborting > > > > Thanks for the help, > > > > Harli > > -- next part -- > > An HTML attachment was scrubbed... > > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20101115/0b3385a5/attachment.htm > > > > -- > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > End of Pw_forum Digest, Vol 41, Issue 28 > > > > > -- > * * * * > Matteo Calandra, Charge de Recherche (CR1) > Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris > Universit? Pierre et Marie Curie, tour 16, case 115 > 4 Place Jussieu, 75252 Paris Cedex 05 France > Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 > http://www.impmc.jussieu.fr/~calandra<http://www.impmc.jussieu.fr/%7Ecalandra> > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101116/c23e178c/attachment.htm
[Pw_forum] MPI_Bcast error from cp.x
Ciao tutti, Pls does anyone know a simple way to fix this error which I got from running cp.x with 4 processors: ERROR: 0032-117 User pack or receive buffer is too small (32) in MPI_Bcast, task 1 ERROR: 0032-117 User pack or receive buffer is too small (16) in MPI_Bcast, task 2 ERROR: 0032-117 User pack or receive buffer is too small (32) in MPI_Bcast, task 3 I googled and found: http://publib.boulder.ibm.com/infocenter/clresctr/vxrx/index.jsp?topic=%2Fcom.ibm.cluster.pe_linux43.messages.doc%2F0032-117.html which says: 0032-117 Parallel Environment for Linux V4.3 Messages SA38-0648-01 User pack or receive buffer too small (number) in string, task number Explanation The buffer specified for the operation was too small to hold the message. In the PACK and UNPACK cases it is the space between current position and buffer end which is too small. User response Increase the size of the buffer or reduce the size of the message. Error Class: MPI_ERR_TRUNCATE I actually don't have a clue in which part of the program I should increase/decrease buffer/message size. Thanks for any help. o. -- * Seek GOD! * -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101116/6bcc4ac1/attachment.htm
