Re: [Wien] Help
That is due to a known bug in WIEN2k 17.1 [ https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17218.html ]. It can be quite the effort to apply the fixes to WIEN2k 17.1 that are mentioned in the mailing list (such as those mentioned at https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17514.html , https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17448.html , and https://github.com/gsabo/WIEN2k-Patches/tree/master/17.1 ). WIEN2k_18 is expected to be released soon [ https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17556.html ]. So, you may want to wait and use that. Regarding the w2web port, it depends on what you need. If each user should not be messing with each others calculation files, then the new port for each user sounds like the better option to me. If each user all need to be working with the same calculation, you could possibly create just one user account dedicated just for WIEN2k and all users of the computer could access that Linux account with the same username and password, then all users have access to start w2web using one port with the same w2web username and password. If each user does need separate accounts, then it depends on who should have control of starting w2web. If you install as root, then only root should be able to start w2web. If installed in user X's account, then usually user Y cannot start w2web, unless you setup file permissions to give user Y access to the files in user X's account. The w2web can be setup so that it is only accessible when you sit in front of the computer at the keyboard (using localhost) or it be setup so that is accessible anywhere in the world (using an ip address) if there are no blocking firewalls. So any user should be able to use the same w2web port locally or remotely, they just have to use the same w2web username and password while their Linux account access username and password are different. So in theory, there are many possibilities for configuring w2web for multiple users. However, WIEN2k calculations can be quite demanding when it comes to hardware resources. It looks like you have a single desktop (or single node) computer. An i7 processor has like 4-6 cores. For small cells, maybe it could handle a few calculation by multiple users. When you get to medium size cells, that hardware might only be enough for one single user. You get to large cell calculations, the calculation likely becomes not feasible or not possible without using a multiple node cluster (multiple computers connect with a GB switch [ https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14035.html ] or a rack server (for example, the Alabama Supercomputer Center's SGI UV has 268 cores! [ https://www.asc.edu/hpc/services/hardware ]). I thought I saw on the Internet some high performance computing (HPC) clusters offering free core hours, but I don't have a list of them. For example, the Sabalcore HPC currently offers 1000 core hours for free: http://www.sabalcore.com/hpc-in-the-cloud-for-academics/ In addition to a cluster having more hardware resources (CPUs, hard drives, RAM modules, etc.) to handle calculations by multiple users, they also have special software (a queuing system) for managing the calculations of multiple users. While it is possible to use w2web with a cluster [ https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01658.html ], typically I haven't seen w2web used with them. One reason for that might be that it may add a security vulnerability point [ https://security.stackexchange.com/questions/178772/what-are-the-possible-ways-to-exploit-a-login-page ]. Though, the main reason is likely because user's come to prefer the convenience and control of using their native job script [ http://susi.theochem.tuwien.ac.at/reg_user/faq/pbs.html ]. Another possible issue with multiple users on your own computer may be that only one user can be logged on locally at a time unless you have it setup so that multiple users can access it using ssh [ https://help.ubuntu.com/lts/serverguide/openssh-server.html ]. An advantage of using an HPC cluster is that there is usually a specialist [ https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17218.html ] who takes care of the ssh setup, manages the system so that you don't have to, and helps you to use it. I would recommend using an HPC cluster for WIEN2k because of that and also because I suspect small cells have been studied to death by researchers such that you may be left with unstudied large cells. Yes, the possible drawback of fights over computing time on the HPC cluster at your local university, company, and/or computing center. The search for a collaborator to use theirs. Been there and had some experience with that. Hopefully that helps and good luck. On 6/21/2018 2:57 PM, Sign In Alert wrote: Good day I hope anyone can help
[Wien] Help
Good day I hope anyone can help me with the following problems. I am working with gfortran installed on linux mint 18.3, (16 GB RAM, 260 GB disk space, intel i7, 2.7 GHz) wien2k 17.1. I just installed wien2k and it seems that the installation went well. So I decided to test the software reproducing the example from the wien2k userguide about TiC. I followed all the steps as indicated, the properties for the DOS, electron charge and X-ray analysis worked well but when I tried the band structured of TiC the plot was not shown properly. According to Dr. Blaha I did not generate the k-mesh or did not executed x lapw1- band (which I did). After generating the file k-band_list I executed the x lapw1 -band. But I hadn't noticed an error that reads:At line 75 of file modules_tmp_.F (unit = 5, file = 'israelperez.in1c') Fortran runtime error: End of file 0.0u 0.0s 0:00.00 0.0% 0+0k 0+0io 0pf+0w error: command /home/israelperez/Apps/Wien2k/lapw1c lapw1.def failed I have no idea what this error is about. I am attaching the corresponding files for reference. The executable lapwc and lapw1.def exist in the Wien2k directory but israelperez.in1c were created in a different directory (i.e. israelperez, the home directory) what can I do? Another problem is that I created another user account (where wien2k is isntalled) and run userconfig_lapw1for this account. My question here is: should I run w2web and generate a new port for each new user after executing userconfig_lapw1? This is what I actually did, as of now I am using one port for the admin and another port for thenew user; is this ok or there is a way to use the same port for all users? I would appreciate any comments you may have. Best regards Israel <> ___ 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 hub-U
Now you copied the error message and then everything is clear: There is a problem in orb with the energy files, when switching from a sequential to a parallel calculation. In wien17.1 when you have a case.dmat* file, you also need case.energyup/dn or with -p a case.eneregyup_1 file. This problem will be fixed in 18.1 In the meantime you could: cp /scratch/WIEN2k17/TEST/T6/T6.energyup /scratch/WIEN2k17/TEST/T6/T6.energyup_1 and the same for dn files. If you don't have a case.energy file either, you have to remove case.dmatup/dn files when starting a -p calculation. Am 21.06.2018 um 20:55 schrieb shaymlal dayananda: Dear Prof. Blaha and Gavin Thank you for your valuable comments. I followed them but I am not successful yet. I am copying case.inorb and case.indmc here. In my system there are two types of U (atom1 and atom 2) and I want to add Hub-U in their f-shells. Please let me know if there are issues in it. CASE.indmc -12. Emin cutoff energy 2 number of atoms for which density matrix is calculated 1 1 3 index of 1st atom, number of L's, L1 2 1 3 dtto for 2nd atom, repeat NATOM times 0 0 r-index, (l,s)index CASE.inorb 1 2 0 nmod, natorb, ipr PRATT 1.0 BROYD/PRATT, mixing 1 1 3 iatom nlorb, lorb 2 1 3 iatom nlorb, lorb 1 nsic 0..AMF, 1..SIC, 2..HFM 0.3307 0.00 U J (Ry) Note: we recommend to use U_eff = U-J and J=0 0.3307 0.00 U J I have attached the job script here with. It has slurm error file. But it doesn't have any clue. (Please see below) Unloading module: Wien2k - Version 17.1 - (Release: 4. July 2017). Loading module: Wien2k - Version 17.1 - (Release: 4. July 2017). Thu Jun 21 13:05:40 EDT 2018 I tested what Prf.Blaha has said about dmat files. But no change happened after coping *dmat* and rerun. my case.dayfile shows below Calculating T6 in /scratch/WIEN2k17/TEST/T6 on gra770 with PID 10447 using WIEN2k_17.1 (Release 30/6/2017) in /home/software/Build_WIEN2k_17.1_M01/bin start (Thu Jun 21 13:05:40 EDT 2018) with lapw0 (140/99 to go) cycle 1 (Thu Jun 21 13:05:40 EDT 2018) (140/99 to go) lapw0 -p (13:05:40) starting parallel lapw0 at Thu Jun 21 13:05:41 EDT 2018 .machine0 : processors running lapw0 in single mode 8.385u 0.319s 0:09.96 87.2% 0+0k 161720+12104io 648pf+0w orb -up -p (13:05:51) 0.001u 0.019s 0:00.12 8.3% 0+0k 7248+32io 23pf+0w error: command /home/software/Build_WIEN2k_17.1_M01/bin/orb uporb.def failed stop error STDOUT is as below. the case.energyup_1 is empty . LAPW0 END forrtl: severe (24): end-of-file during read, unit 14, file /scratch/WIEN2k17/TEST/T6/T6.energyup_1 Image PC Routine Line Source orb 004166C8 Unknown Unknown Unknown orb 0043 Unknown Unknown Unknown orb 0040AB4A init_ 279 init.f orb 00402C65 MAIN__ 103 main.f orb 004027AE Unknown Unknown Unknown libc.so.6 2AAC761432E0 Unknown Unknown Unknown orb 004026AA Unknown Unknown Unknown stop error Thank you Daya On Wednesday, June 20, 2018 6:17 AM, Gavin Abo wrote: Hi, You seem to have sent this once: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17580.html Twice: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17581.html Three times: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17584.html The "Error in Vorb" error is usually due to something wrong with your case.inorb or case.indm(c) file: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17583.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg10408.html Another possible cause of the "Error in Vorb" error might be a problem with the dmat files: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg10492.html Did you check the standard error/output files for any forrtl errors [ https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17585.html ]? Kind Regards, Gavin On 6/19/2018 11:15 PM, shaymlal dayananda wrote: Dear developers and users We have recently got installed WIEN2k 17.1 and it uses slurm job submission manager. I am trying to do some test cases. Unfortunately our computer supporters could not make the job submission script with interface, so I do it manually. I tested the scf calculation with " runsp_lapw -NI -p -ec 0.0001 -cc 0.001 ". It completed without problem. However for adding hubbard-U , job crashes. I have created case.indm, case.indmc
Re: [Wien] error in hub-U
Dear Prof. Blaha and Gavin Thank you for your valuable comments. I followed them but I am not successful yet.>I am copying case.inorb and case.indmc here. In my system there are two types of U (atom1 and atom 2) and I want to add Hub-U in their f-shells. Please let me know if there are issues in it. CASE.indmc-12. Emin cutoff energy 2 number of atoms for which density matrix is calculated 1 1 3 index of 1st atom, number of L's, L1 2 1 3 dtto for 2nd atom, repeat NATOM times 0 0 r-index, (l,s)index CASE.inorb 1 2 0 nmod, natorb, ipr PRATT 1.0 BROYD/PRATT, mixing 1 1 3 iatom nlorb, lorb 2 1 3 iatom nlorb, lorb 1 nsic 0..AMF, 1..SIC, 2..HFM 0.3307 0.00 U J (Ry) Note: we recommend to use U_eff = U-J and J=0 0.3307 0.00 U J >>I have attached the job script here with. It has slurm error file. >>But it doesn't have any clue. (Please see below) Unloading module: Wien2k - Version 17.1 - (Release: 4. July 2017). Loading module: Wien2k - Version 17.1 - (Release: 4. July 2017). Thu Jun 21 13:05:40 EDT 2018 >I tested what Prf.Blaha has said about dmat files. But no change happened >after coping *dmat* and rerun. my case.dayfile shows below Calculating T6 in /scratch/WIEN2k17/TEST/T6 on gra770 with PID 10447 using WIEN2k_17.1 (Release 30/6/2017) in /home/software/Build_WIEN2k_17.1_M01/bin start (Thu Jun 21 13:05:40 EDT 2018) with lapw0 (140/99 to go) cycle 1 (Thu Jun 21 13:05:40 EDT 2018) (140/99 to go) > lapw0 -p (13:05:40) starting parallel lapw0 at Thu Jun 21 13:05:41 EDT >2018 .machine0 : processors running lapw0 in single mode 8.385u 0.319s 0:09.96 87.2% 0+0k 161720+12104io 648pf+0w > orb -up -p (13:05:51) 0.001u 0.019s 0:00.12 8.3% 0+0k 7248+32io >23pf+0w error: command /home/software/Build_WIEN2k_17.1_M01/bin/orb uporb.def failed > stop error STDOUT is as below. the case.energyup_1 is empty . LAPW0 END forrtl: severe (24): end-of-file during read, unit 14, file /scratch/WIEN2k17/TEST/T6/T6.energyup_1 Image PC Routine Line Source orb 004166C8 Unknown Unknown Unknown orb 0043 Unknown Unknown Unknown orb 0040AB4A init_ 279 init.f orb 00402C65 MAIN__ 103 main.f orb 004027AE Unknown Unknown Unknown libc.so.6 2AAC761432E0 Unknown Unknown Unknown orb 004026AA Unknown Unknown Unknown > stop error Thank you Daya On Wednesday, June 20, 2018 6:17 AM, Gavin Abo wrote: Hi, You seem to have sent this once: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17580.html Twice: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17581.html Three times: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17584.html The "Error in Vorb" error is usually due to something wrong with your case.inorb or case.indm(c) file: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17583.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg10408.html Another possible cause of the "Error in Vorb" error might be a problem with the dmat files: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg10492.html Did you check the standard error/output files for any forrtl errors [https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17585.html ]? Kind Regards, Gavin On 6/19/2018 11:15 PM, shaymlal dayananda wrote: Dear developers and users We have recently got installed WIEN2k 17.1 and it uses slurm job submission manager. I am trying to do some test cases. Unfortunately our computer supporters could not make the job submission script with interface, so I do it manually. I tested the scf calculation with " runsp_lapw -NI -p -ec 0.0001 -cc 0.001 ". It completed without problem. However for adding hubbard-U , job crashes. I have created case.indm, case.indmc and case.inorb file and used the command "runsp_lapw -NI -p -dm -orb -ec 0.0001 -cc 0.001" in the job script. It failed with error "Error in Vorb" in uporb.error. I couldn't find any message in any relevant file. But it runs in single mode with "runsp_lapw -NI -p -dm -orb -ec 0.0001 -cc 0.001". Please help me to get corrected the parallel mode calculation. I appreciate any advice. I copied the dayfile and the uporb.def in my parallel mode calculation. case.dayfile is ; Calculating U3O8-8.5-5000 in /scratch/WIEN2k17/UB-8.5-5000 on gra144 with PID 28448 using
