[Pw_forum] "xspectra.x" crashed with segmentation fault
PWSCF Forum > Message-ID: <7F4B01A5-0DC1-457A-9A67-A8A2F9D19D8D at democritos.it> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > > On Jul 20, 2011, at 18:52 , Abdulrafiu Raji wrote: > > > cannot open /home/araji/XAS_SiO2_scr.1/qtz_ar1SCF_kp2.save/ > > charge-density.dat file > > it is not there, or it is corrupted, or empty, or not in the right > format. > Note that it is a binary file that should be written by and read by > executables compiled with the same compiler on th same machine, > as a rule > > P. > --- > Paolo Giannozzi, Dept of Chemistry, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110722/5fed7161/attachment.htm
[Pw_forum] Pw_forum Digest, Vol 49, Issue 53
Thanks Paolo, you are absolutely right!...I was running the XANES script with mpirun. However, I tried to run the script again, serially, by doing the following: I copied the QE version 4.2.1 to my home directory on a HPC, and compiled Xspectra code using:'make xspectra'. The resulting 'xspectra.x' was then copied into my home directory: 'home/araji/xspectra.x' and the job was submitted using the script below. However, the code stopped again, just after starting with the error message (please find below). The shell script for submitting the job) is also appended. I repeat once again that I used the same version of the code for both the 'scf' and 'xanes' calculations. Thank you very much. ... A. T. Raji ICTP, Trieste. Italy. === Program XSPECTRA v.4.2.1 starts on 20Jul2011 at 18:39:37 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please acknowledge "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org;, in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO bef %% from read_rho_xml : error # 1 cannot open /home/araji/XAS_SiO2_scr.1/qtz_ar1SCF_kp2.save/charge-density.dat file for reading === #PBS -N SiO2.XAS_pln_kpt_2.in ### Number and which of nodes as well as number of CPUs per node: #PBS -l nodes=1:ppn=8 ### resource limits: amount of memory and CPU time ([[h:]m:]s). ### Queue name (default, ib, ...) #PBS -q serial # ### This job's working directory echo "Working directory is $PBS_O_WORKDIR" cd /home/araji/XAS_SiO2 echo Running on host `hostname` echo Time is `date` echo Directory is `pwd` ## Run your executable ##. /etc/profile.d/modules.sh module load espresso/4.2.1/openmpi/1.4.3/gnu ###module load openmpi/1.4.3/gnu/4.4.0 /home/araji/xspectra.x < SiO2.XAS_pln_kpt_2.in > SiO2.XAS_pln_kpt_2.out = calculation='scf', restart_mode='from_scratch', pseudo_dir = '/home/araji/pseudo/', outdir = '/home/araji/XAS_SiO2_scr.1/', prefix ='qtz_ar1SCF_kp2', verbosity = 'high', wf_collect = .true., . . . K_POINTS (automatic) 2 2 2 0 0 0 = _xspectra calculation='xanes_dipole' prefix='qtz_ar1SCF_kp2', outdir='/home/araji/XAS_SiO2_scr.1/', xonly_plot=.false., xniter=2000, xcheck_conv=50, xepsilon(1)=1.0, xepsilon(2)=1.0, xepsilon(3)=0.0, xiabs=1, x_save_file='SiO2.XAS.pln.sav', xread_wf=.false., ef_r=0.402521132, xerror=0.001, wf_collect=.true., . . . . . _occ cut_desmooth=0.1, 3 3 3 0 0 0 > === > . Re: Problem with XSPECTRA: file can't open (Paolo Giannozzi) > > Message: 1 > Date: Tue, 19 Jul 2011 19:08:32 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Problem with XSPECTRA: file can't open > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Let me guess: you are running in parallel (with mpirun or > mpiexec) an executable compiled for serial execution > > P. > --- > Paolo Giannozzi, Dept of Chemistry, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110720/e0d82cbc/attachment-0001.htm
[Pw_forum] Problem with XSPECTRA: file can't open
Dear QE users, I was trying to run the Xspectra.x code on a linux cluster machine. However, the xspectra.x code stops just after it starts with some error messages (please find below). I used the same version of the code for the 'scf' and xanes-dipole calculations, i.e. version 4.2.1. You will observed that I have not done much modifications to the 'xanes-dipole' input file given in the examples, in the code. The present calculations are suppose to be dry runs for more realistic calculations. You will also find below, input files for the scf and 'xanes-dipole' used for the runs. I guarantee that the relevant directories/files exist. Thank you for your attention. Abdulrafiu Raji, ICTP, Trieste, Italy. == Program XSPECTRA v.4.2.1 starts on 19Jul2011 at 17:45: 8 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please acknowledge "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org;, in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO bef Program XSPECTRA v.4.2.1 starts on 19Jul2011 at 17:45: 8 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please acknowledge "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org;, in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO %% from input_xspectra : error # 1 reading input_xspectra namelist %% stopping ... Program XSPECTRA v.4.2.1 starts on 19Jul2011 at 17:45: 8 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please acknowledge "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org;, in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO %% from input_xspectra : error # 1 reading input_xspectra namelist %% stopping ... Program XSPECTRA v.4.2.1 starts on 19Jul2011 at 17:45: 8 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please acknowledge "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org;, in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO %% from input_xspectra : error # 1 reading input_xspectra namelist %% stopping ... Program XSPECTRA v.4.2.1 starts on 19Jul2011 at 17:45: 8 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please acknowledge "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org;, in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO %% from input_xspectra : error # 1 reading input_xspectra namelist %% stopping ... Program XSPECTRA v.4.2.1 starts on 19Jul2011 at 17:45: 8 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please acknowledge "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org;, in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO %% from input_xspectra : error # 1 reading input_xspectra namelist %% stopping ... Program XSPECTRA v.4.2.1 starts on 19Jul2011 at 17:45: 8 This program is part of th
[Pw_forum] Can't run any example in QE v4.0.4
Dear users, I have just downloaded QE v4.0.4. After successful compilation on my AMD dual- processor, I tried to run some examples in the code. But each time I do this, the following error messages are reported, and this is case of may examples that I have tried : running cp.x as: mpirun -np 2 /home/araji/Codes/espresso-4.0.5/bin/cp.x cleaning /home/araji/tmp... done running the calculation with fixed ions/run_example: line 131: mpirun: command not found How do I handle this? I should mention that I have been able to run the examples on earlier versions, v.4.0.3, e.t.c, without any hitch. Thanks for your attention. Abdulrafiu Tunde Raji. Physics Department. University of Cape Town. South Africa. Raji Abdulrafiu Tunde, Department of Physics, University of Cape Town (RW James Bld.),Private Bag X3, Rondebosch 7701, Cape Town. South Africa. Office number : Rm. 522 Cell: +27722668228 Fax: +27216503342 __ UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 4500. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity. _
[Pw_forum] QHA Code
Dear Prof Eyvaz Isaev, Kindly send the QHA code to me as well. I made a request for this code to you, through an e-mail about two months back.Thanks for your anticipated cooperation. Raji Abdulrafiu Tunde, Condensed Matter and Material Physics Group, Department of Physics, University of Cape Town, Rondebosch 7701, Cape Town. South Africa. Raji Abdulrafiu Tunde, Department of Physics, University of Cape Town (RW James Bld.),Private Bag X3, Rondebosch 7701, Cape Town. South Africa. Office number : Rm. 522 Cell: +27722668228 Fax: +27216503342 __ UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 4500. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity. _
[Pw_forum] How to handle the i/o error in davcio problem in NEB calculations
Dear fellow Pwscf users, I was using the QE vers.3.2.3 (parallel) to do NEB calculations. At the 11th iterations, and while relaxing the 4th image, it suddenly stopped with the following error message: %% from davcio : error #10 i/o error in davcio %% stopping ... %% Also, "restart_mode = restart" in my input file, since the calculation had earlier stopped because the CPU time was over. I observed that similar problem was reported on this forum, and the response (by Carlo Sbraccia) was that the files in '$outdir' directory should be removed since the restart file for neb calculations is that with '.path' extension in the working directory. I implemented Carlo's suggestions and removed all the files in the scratch directory with prefixes of my calculations, and the program was then restarted. But on getting to 4th image, while carrying out the 12th iterations, it stopped again, displaying the similar error message as quoted above. Can anyone please advise on what I must do next? Thank you very much. Abdulrafiu Tunde Raji, Dept. of Physics, University of Cape Town, Rondebosch 7701, Cape Town, South Africa. Raji Abdulrafiu Tunde, Department of Physics, University of Cape Town (RW James Bld.),Private Bag X3, Rondebosch 7701, Cape Town. South Africa. Office number : Rm. 522 Cell: +27722668228 Fax: +27216503342
