Re: [Wien] Error in mpi+k point parallelization across multiple nodes
You appear to be missing the line setenv WIEN_MPIRUN=... This is setup when you run siteconfig, and provides the information on how mpi is run on your system. N.B., did you setup and compile the mpi code? ___ Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu MURI4D.numis.northwestern.edu Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi On Apr 28, 2015 4:22 AM, lung Fermin ferminl...@gmail.com wrote: Dear Wien2k community, I am trying to perform calculation on a system of ~100 in-equivalent atoms using mpi+k point parallelization on a cluster. Everything goes fine when the program was run on a single node. However, if I perform the calculation across different nodes, the follow error occurs. How to solve this problem? I am a newbie to mpi programming, any help would be appreciated. Thanks. The error message (MVAPICH2 2.0a): --- Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1 -13 z1-13 z1-13 z1-13 z1-13 z1-13 number of processors: 32 LAPW0 END [z1-2:mpirun_rsh][process_mpispawn_connection] mpispawn_0 from node z1-13 aborted: Error while reading a PMI socket (4) [z1-13:mpispawn_0][child_handler] MPI process (rank: 11, pid: 8546) terminated with signal 9 - abort job [z1-13:mpispawn_0][readline] Unexpected End-Of-File on file descriptor 8. MPI process died? [z1-13:mpispawn_0][mtpmi_processops] Error while reading PMI socket. MPI process died? [z1-2:mpispawn_0][readline] Unexpected End-Of-File on file descriptor 12. MPI process died? [z1-2:mpispawn_0][mtpmi_processops] Error while reading PMI socket. MPI process died? [z1-2:mpispawn_0][child_handler] MPI process (rank: 0, pid: 35454) terminated with signal 9 - abort job [z1-2:mpirun_rsh][process_mpispawn_connection] mpispawn_0 from node z1-2 aborted: MPI process error (1) [cli_15]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 15 stop error -- The .machines file: # 1:z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 1:z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 granularity:1 extrafine:1 The parallel_options: setenv TASKSET no setenv USE_REMOTE 0 setenv MPI_REMOTE 1 setenv WIEN_GRANULARITY 1 Thanks. Regards, Fermin ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Error in mpi+k point parallelization across multiple nodes
Thanks for Prof. Marks' comment. 1. In the previous email, I have missed to copy the line setenv WIEN_MPIRUN /usr/local/mvapich2-icc/bin/mpirun -np _NP_ -hostfile _HOSTS_ _EXEC_ It was in the parallel_option. Sorry about that. 2. I have checked that the running program was lapw1c_mpi. Besides, when the mpi calculation was done on a single node for some other system, the results are consistent with the literature. So I believe that the mpi code has been setup and compiled properly. Would there be something wrong with my option in siteconfig..? Do I have to set some command to bind the job? Any other possible cause of the error? Any suggestions or comments would be appreciated. Thanks. Regards, Fermin You appear to be missing the line setenv WIEN_MPIRUN=... This is setup when you run siteconfig, and provides the information on how mpi is run on your system. N.B., did you setup and compile the mpi code? ___ Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu MURI4D.numis.northwestern.edu Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi On Apr 28, 2015 4:22 AM, lung Fermin ferminl...@gmail.com wrote: Dear Wien2k community, I am trying to perform calculation on a system of ~100 in-equivalent atoms using mpi+k point parallelization on a cluster. Everything goes fine when the program was run on a single node. However, if I perform the calculation across different nodes, the follow error occurs. How to solve this problem? I am a newbie to mpi programming, any help would be appreciated. Thanks. The error message (MVAPICH2 2.0a): --- Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1 -13 z1-13 z1-13 z1-13 z1-13 z1-13 number of processors: 32 LAPW0 END [z1-2:mpirun_rsh][process_mpispawn_connection] mpispawn_0 from node z1-13 aborted: Error while reading a PMI socket (4) [z1-13:mpispawn_0][child_handler] MPI process (rank: 11, pid: 8546) terminated with signal 9 - abort job [z1-13:mpispawn_0][readline] Unexpected End-Of-File on file descriptor 8. MPI process died? [z1-13:mpispawn_0][mtpmi_processops] Error while reading PMI socket. MPI process died? [z1-2:mpispawn_0][readline] Unexpected End-Of-File on file descriptor 12. MPI process died? [z1-2:mpispawn_0][mtpmi_processops] Error while reading PMI socket. MPI process died? [z1-2:mpispawn_0][child_handler] MPI process (rank: 0, pid: 35454) terminated with signal 9 - abort job [z1-2:mpirun_rsh][process_mpispawn_connection] mpispawn_0 from node z1-2 aborted: MPI process error (1) [cli_15]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 15 stop error -- The .machines file: # 1:z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 1:z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 granularity:1 extrafine:1 The parallel_options: setenv TASKSET no setenv USE_REMOTE 0 setenv MPI_REMOTE 1 setenv WIEN_GRANULARITY 1 Thanks. Regards, Fermin ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Error in mpi+k point parallelization across multiple nodes
Unfortunately it is hard to know what is going on. A google search on Error while reading PMI socket. indicates that the message you have means it did not work, and is not specific. Some suggestions: a) Try mpiexec (slightly different arguments). You just edit parallel_options. https://wiki.mpich.org/mpich/index.php/Using_the_Hydra_Process_Manager b) Try an older version of mvapich2 if it is on the system. c) Do you have to launch mpdboot for your system https://wiki.calculquebec.ca/w/MVAPICH2/en? d) Talk to a sys_admin, particularly the one who setup mvapich e) Do cat *.error, maybe something else went wrong or it is not mpi's fault but a user error. ___ Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu MURI4D.numis.northwestern.edu Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi On Apr 28, 2015 10:17 PM, lung Fermin ferminl...@gmail.com wrote: Thanks for Prof. Marks' comment. 1. In the previous email, I have missed to copy the line setenv WIEN_MPIRUN /usr/local/mvapich2-icc/bin/mpirun -np _NP_ -hostfile _HOSTS_ _EXEC_ It was in the parallel_option. Sorry about that. 2. I have checked that the running program was lapw1c_mpi. Besides, when the mpi calculation was done on a single node for some other system, the results are consistent with the literature. So I believe that the mpi code has been setup and compiled properly. Would there be something wrong with my option in siteconfig..? Do I have to set some command to bind the job? Any other possible cause of the error? Any suggestions or comments would be appreciated. Thanks. Regards, Fermin You appear to be missing the line setenv WIEN_MPIRUN=... This is setup when you run siteconfig, and provides the information on how mpi is run on your system. N.B., did you setup and compile the mpi code? ___ Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu MURI4D.numis.northwestern.edu Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi On Apr 28, 2015 4:22 AM, lung Fermin ferminl...@gmail.com wrote: Dear Wien2k community, I am trying to perform calculation on a system of ~100 in-equivalent atoms using mpi+k point parallelization on a cluster. Everything goes fine when the program was run on a single node. However, if I perform the calculation across different nodes, the follow error occurs. How to solve this problem? I am a newbie to mpi programming, any help would be appreciated. Thanks. The error message (MVAPICH2 2.0a): --- Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1 -13 z1-13 z1-13 z1-13 z1-13 z1-13 number of processors: 32 LAPW0 END [z1-2:mpirun_rsh][process_mpispawn_connection] mpispawn_0 from node z1-13 aborted: Error while reading a PMI socket (4) [z1-13:mpispawn_0][child_handler] MPI process (rank: 11, pid: 8546) terminated with signal 9 - abort job [z1-13:mpispawn_0][readline] Unexpected End-Of-File on file descriptor 8. MPI process died? [z1-13:mpispawn_0][mtpmi_processops] Error while reading PMI socket. MPI process died? [z1-2:mpispawn_0][readline] Unexpected End-Of-File on file descriptor 12. MPI process died? [z1-2:mpispawn_0][mtpmi_processops] Error while reading PMI socket. MPI process died? [z1-2:mpispawn_0][child_handler] MPI process (rank: 0, pid: 35454) terminated with signal 9 - abort job [z1-2:mpirun_rsh][process_mpispawn_connection] mpispawn_0 from node z1-2 aborted: MPI process error (1) [cli_15]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 15 stop error -- The .machines file: # 1:z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 1:z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 granularity:1 extrafine:1 The parallel_options: setenv TASKSET no setenv USE_REMOTE 0 setenv MPI_REMOTE 1 setenv WIEN_GRANULARITY 1 Thanks. Regards, Fermin
Re: [Wien] Discrepancy between DoS plot and bandstructure plot for position of fermi level
Respected Prof. Blaha and Gavin Abo sir, I followed your suggestions and problem is resolved. Thanking you again for helping me out. Yours sincerely, Saurabh Samant On Tue, Apr 28, 2015 at 11:57 PM, Gavin Abo gs...@crimson.ua.edu wrote: Remove -orb from the 'x lapw1' steps: http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg10757.html http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg09117.html http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg02807.html On 4/28/2015 11:44 AM, saurabh samant wrote: Respected Peter Blaha Sir, I have plotted the bandstructure in w2web with the following commands: 1. Create fecr2s4ggau.klist band 2. x lapw1 -band -up -orb 3. x lapw1 -band -dn -orb 4. x lapwso -up -orb 5. edit fecr2s4ggau.insp 6. x spaghetti -up -so 7. plot bandstructure Sir, eagerly waiting for your help and directions. Thanking You, Yours sincerely Saurabh Samant On Tue, Apr 28, 2015 at 10:48 PM, Peter Blaha pbl...@theochem.tuwien.ac.at wrote: How did you create the bandstructure plot ? Please describe the sequence of commands. It looks as if you did not plot the spin-orbit splitted bands ? Am 27.04.2015 um 09:49 schrieb saurabh samant: Dear WIEN2k users, I have done a spin-polarized GGA+SO+U calculation for an AB2S4 compound. The fermi level at the dosplot is at the top of valence band but in the bandstructureplot the fermi level is at the middle of the valence and conduction band. But as far as I know it should be at the top of valence band. So,why is this discrepancy. Plz help to fix this problem. I am also attaching dosplot and bandstructure plot for your reference. Thanking You, Yours sincerely Saurabh Samanta Ph.D. candidate NIT Raipur ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] U , J and effective U
I think U should stay the same because U is the interaction parameter. The
correction to the total DFT energy due to the on-site repulsion is U\sum
n_{m\sigma} n_{m'\sigma'}-double counting, if I remember it correctly. So
even if we use the same U for both spin channels, the spin-up electron and
spin-down electron would still be under different effective field, i.e. the
intraatomic correlation are different for different spins. This is my
understanding, which may be incorrect.
On Tue, Apr 28, 2015 at 12:09 PM, delamora delam...@unam.mx wrote:
Dear WIEN2k community,
I have a discussion with my Professor, John B Goodenough, and I
would like to share with you.
Is the U or the effective U (U-J) the same for up and down spin?
We are working in ruthenates and in some cases they are half
metals, so the mobility of the up and down spins is different so the
intraatomic correlation should be also different.
Yours
Pablo de la Mora
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Re: [Wien] Discrepancy between DoS plot and bandstructure plot for position of fermi level
How did you create the bandstructure plot ? Please describe the sequence of commands. It looks as if you did not plot the spin-orbit splitted bands ? Am 27.04.2015 um 09:49 schrieb saurabh samant: Dear WIEN2k users, I have done a spin-polarized GGA+SO+U calculation for an AB2S4 compound. The fermi level at the dosplot is at the top of valence band but in the bandstructureplot the fermi level is at the middle of the valence and conduction band. But as far as I know it should be at the top of valence band. So,why is this discrepancy. Plz help to fix this problem. I am also attaching dosplot and bandstructure plot for your reference. Thanking You, Yours sincerely Saurabh Samanta Ph.D. candidate NIT Raipur ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- Peter Blaha Inst.Materials Chemistry TU Vienna Getreidemarkt 9 A-1060 Vienna Austria +43-1-5880115671 ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Discrepancy between DoS plot and bandstructure plot for position of fermi level
Respected Peter Blaha Sir, I have plotted the bandstructure in w2web with the following commands: 1. Create fecr2s4ggau.klist band 2. x lapw1 -band -up -orb 3. x lapw1 -band -dn -orb 4. x lapwso -up -orb 5. edit fecr2s4ggau.insp 6. x spaghetti -up -so 7. plot bandstructure Sir, eagerly waiting for your help and directions. Thanking You, Yours sincerely Saurabh Samant On Tue, Apr 28, 2015 at 10:48 PM, Peter Blaha pbl...@theochem.tuwien.ac.at wrote: How did you create the bandstructure plot ? Please describe the sequence of commands. It looks as if you did not plot the spin-orbit splitted bands ? Am 27.04.2015 um 09:49 schrieb saurabh samant: Dear WIEN2k users, I have done a spin-polarized GGA+SO+U calculation for an AB2S4 compound. The fermi level at the dosplot is at the top of valence band but in the bandstructureplot the fermi level is at the middle of the valence and conduction band. But as far as I know it should be at the top of valence band. So,why is this discrepancy. Plz help to fix this problem. I am also attaching dosplot and bandstructure plot for your reference. Thanking You, Yours sincerely Saurabh Samanta Ph.D. candidate NIT Raipur ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- Peter Blaha Inst.Materials Chemistry TU Vienna Getreidemarkt 9 A-1060 Vienna Austria +43-1-5880115671 ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] U , J and effective U
Dear WIEN2k community, I have a discussion with my Professor, John B Goodenough, and I would like to share with you. Is the U or the effective U (U-J) the same for up and down spin? We are working in ruthenates and in some cases they are half metals, so the mobility of the up and down spins is different so the intraatomic correlation should be also different. Yours Pablo de la Mora ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Discrepancy between DoS plot and bandstructure plot for position of fermi level
Remove -orb from the 'x lapw1' steps: http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg10757.html http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg09117.html http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg02807.html On 4/28/2015 11:44 AM, saurabh samant wrote: Respected Peter Blaha Sir, I have plotted the bandstructure in w2web with the following commands: 1. Create fecr2s4ggau.klist band 2. x lapw1 -band -up -orb 3. x lapw1 -band -dn -orb 4. x lapwso -up -orb 5. edit fecr2s4ggau.insp 6. x spaghetti -up -so 7. plot bandstructure Sir, eagerly waiting for your help and directions. Thanking You, Yours sincerely Saurabh Samant On Tue, Apr 28, 2015 at 10:48 PM, Peter Blaha pbl...@theochem.tuwien.ac.at mailto:pbl...@theochem.tuwien.ac.at wrote: How did you create the bandstructure plot ? Please describe the sequence of commands. It looks as if you did not plot the spin-orbit splitted bands ? Am 27.04.2015 um 09:49 schrieb saurabh samant: Dear WIEN2k users, I have done a spin-polarized GGA+SO+U calculation for an AB2S4 compound. The fermi level at the dosplot is at the top of valence band but in the bandstructureplot the fermi level is at the middle of the valence and conduction band. But as far as I know it should be at the top of valence band. So,why is this discrepancy. Plz help to fix this problem. I am also attaching dosplot and bandstructure plot for your reference. Thanking You, Yours sincerely Saurabh Samanta Ph.D. candidate NIT Raipur ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] a rhombohedral structure
Dear Dr. Marks I attached here case.struct. Thanks From: Laurence Marks l-ma...@northwestern.edu To: A Mailing list for WIEN2k users wien@zeus.theochem.tuwien.ac.at Sent: Tuesday, April 28, 2015 7:05 AM Subject: Re: [Wien] a rhombohedral structure What are the rmt's? Attach your struct file.___ Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu MURI4D.numis.northwestern.edu Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-GyorgiOn Apr 27, 2015 9:25 PM, Hajar Nejati hajar.nejatip...@yahoo.com wrote: Dear Dr. Blaha and wien2k users I have problem for making the case. struct for In2O3 in rhombohedral crystal with spacegroup R-3c (167) and these parameters:a=b=5.4928, c= 14.4242In position: 12c (0, 0, 0.3576)O position: 18e (0.2961, 0, 0.25) With the default Rmt in w2web, the charge of In leaks out. Increasing the Rmt leads to the nn error.Can help me for making this struct? The best ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html r3c.struct Description: Binary data ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Discrepancy between DoS plot and bandstructure plot for position of fermi level
On Mon, 2015-04-27 at 13:19 +0530, saurabh samant wrote: Dear WIEN2k users, I have done a spin-polarized GGA+SO+U calculation for an AB2S4 compound. The fermi level at the dosplot is at the top of valence band but in the bandstructureplot the fermi level is at the middle of the valence and conduction band. But as far as I know it should be at the top of valence band. So,why is this discrepancy. Plz help to fix this problem. I am also attaching dosplot and bandstructure plot for your reference. Thanking You, Yours sincerely Saurabh Samanta Ph.D. candidate NIT Raipur Dear Saurabh, For spaghetti plot you need to insert correct Fermi energy (Ry) into the case.insp file manually, so I guess you just inserted the wrong value there. Check you scf files for :FER line. Best regards Pavel ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] a rhombohedral structure
Thank you so so much dear Gavin Abo.I got your reply and applied that successfully. The best for you Sincerely yoursHajar 1) Go to: http://www.cryst.ehu.es/cryst/get_wp.html 2) Put 167 in the box and click ITA Settings 3) Click the R-3c :r link 4) In the table, you should see 12c (0,0,z) for the hexagonal setting and 12c (z,z,z) for the rhombohedral setting. Your In atomic position appears to be in the hexagonal setting 12c (0,0,z), where z = 0.3576. In Wien2k for R spacegroups (like R-3c), you to have to enter the atomic positions in the rhombohedral setting [ http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg05554.html ]. Did you enter in StructGen the atomic positions in the rhombohedral setting? On 4/27/2015 8:20 PM, Hajar Nejati wrote: Dear Dr. Blaha and wien2k users I have problem for making the case. struct for In2O3 in rhombohedral crystal with spacegroup R-3c (167) and these parameters: a=b=5.4928, c= 14.4242 In position: 12c (0, 0, 0.3576) O position: 18e (0.2961, 0, 0.25) With the default Rmt in w2web, the charge of In leaks out. Increasing the Rmt leads to the nn error. Can help me for making this struct? The best ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] Error in mpi+k point parallelization across multiple nodes
Dear Wien2k community, I am trying to perform calculation on a system of ~100 in-equivalent atoms using mpi+k point parallelization on a cluster. Everything goes fine when the program was run on a single node. However, if I perform the calculation across different nodes, the follow error occurs. How to solve this problem? I am a newbie to mpi programming, any help would be appreciated. Thanks. The error message (MVAPICH2 2.0a): --- Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1 -13 z1-13 z1-13 z1-13 z1-13 z1-13 number of processors: 32 LAPW0 END [z1-2:mpirun_rsh][process_mpispawn_connection] mpispawn_0 from node z1-13 aborted: Error while reading a PMI socket (4) [z1-13:mpispawn_0][child_handler] MPI process (rank: 11, pid: 8546) terminated with signal 9 - abort job [z1-13:mpispawn_0][readline] Unexpected End-Of-File on file descriptor 8. MPI process died? [z1-13:mpispawn_0][mtpmi_processops] Error while reading PMI socket. MPI process died? [z1-2:mpispawn_0][readline] Unexpected End-Of-File on file descriptor 12. MPI process died? [z1-2:mpispawn_0][mtpmi_processops] Error while reading PMI socket. MPI process died? [z1-2:mpispawn_0][child_handler] MPI process (rank: 0, pid: 35454) terminated with signal 9 - abort job [z1-2:mpirun_rsh][process_mpispawn_connection] mpispawn_0 from node z1-2 aborted: MPI process error (1) [cli_15]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 15 stop error -- The .machines file: # 1:z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 z1-2 1:z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 z1-13 granularity:1 extrafine:1 The parallel_options: setenv TASKSET no setenv USE_REMOTE 0 setenv MPI_REMOTE 1 setenv WIEN_GRANULARITY 1 Thanks. Regards, Fermin ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Discrepancy between DoS plot and bandstructure plot for position of fermi level
Dear WIEN2k users, I inserted the fermi level for gga+orb+so correctly in case.insp from w2web as follows: Header from fecr2s4ggau.qtlup and possible FERMI energies: ATOM 1: Fe: tot,s,p,PZ,PX+PY,d,DZ2,DXY,DX2Y2,DXZ+DYZ,f ATOM 2: Cr: tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM 3: S: tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f /home/saurabh/WIEN2k/fecr2s4ggau/fecr2s4ggau.scf: EF (TETRAH.M.)= 0.4336395010 /home/saurabh/WIEN2k/fecr2s4ggau/gga.scf: EF (TETRAH.M.)= 0.4317226275 ### Figure configuration 5.0 3.0 # paper offset of plot 10.0 15.0 # xsize,ysize [cm] 1.0 4 # major ticks, minor ticks 1.0 1 # character height, font switch 1.1 24 # line width, line switch, color switch ### Data configuration -14.0 8.0 2 # energy range, energy switch (1:Ry, 2:eV) 1 0.4336 # Fermi switch, Fermi-level (in Ry units) 1 999# number of bands for heavier plotting 1,1 0 10.2# jatom, jtype, size of heavier plotting Fermi switch: 0...no line 1...solid line 2...dashed line 3...dotted line Line switch: 0...dots 1...lines 2...lines and open circle 3...lines and filled circles Color switch (re-define your colors in defins.f) 0...black 1...one-color plot 2...three-color plot 3...multi-color plot 4...multi-color plot, one color for each irr. representations Font switch: 0...no text 1...Times and Symbol 2...Times, Symbol, and Times-Italic 3...Helvetica, Symbol, and Helvetica-Italic 4...(include your own fonts in defins.f) Also, the fermi level in scf files is as follows: Analysis of parameter: :FER in fecr2s4ggau.scf (showing last 50 / 1 lines) --- FER --- :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4312602195 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4312602195 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4489755053 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4489755053 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4551114771 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4551114771 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4590074438 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4590074438 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4497480616 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4497480616 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4540730620 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4540730620 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4650339392 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4650339392 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4562220956 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4562220956 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4430868924 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4430868924 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.441865 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.441865 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4448929029 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4448929029 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4432347850 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4432347850 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4381252265 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4381252265 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4405614152 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4405614152 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4273995777 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4273995777 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4355275990 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4355275990 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4352041844 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4352041844 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4340355980 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4340355980 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4334836163 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4334836163 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4336395010 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.4336395010 Sir, looking forward for your help to fix this problem. With regards, Saurabh Samant Ph.D. candidate NIT Raipur On Tue, Apr 28, 2015 at 12:35 PM, Pavel Ondracka pavel.ondra...@email.cz wrote: On Mon, 2015-04-27 at 13:19 +0530, saurabh samant wrote: Dear WIEN2k users, I have done a spin-polarized GGA+SO+U calculation for an AB2S4 compound. The fermi level at the dosplot is at the top of valence band but in the bandstructureplot the fermi level is at the middle of the valence and conduction band. But as far as I know it should be at the top of valence band. So,why is this discrepancy. Plz help to fix this problem. I am also attaching dosplot and bandstructure plot for your reference. Thanking You, Yours sincerely Saurabh Samanta Ph.D. candidate NIT Raipur Dear Saurabh, For spaghetti plot you need to insert correct Fermi energy (Ry) into the case.insp file manually, so I guess you
