[Wien] XCrysDen in w2web?
Dear Prof. Blaha, The suggested procedure works fine. Thank you very much, Jianxin On Jan 9, 2010, at 7:05 AM, Peter Blaha wrote: > At "localhost" issue: > > ssh -X hostname_where_w2web_runs(the -X option directs the X- > windows system to open screens on loc.host) > ps -ef |grep w2web > kill (kill all pids with w2web) > w2web > > now you can reconnect with your browser to w2web and xcrysden should > open on localhost. > > Alternatively xcrysden can always be called from a terminal: > > ssh -X w2web_host (again -X is necessary!!!) > cd case-directory > xcrysden --wien_struct . > (Try also xcrysden --help to see all options) > > >> I have a problem using XCrysDen in w2web remotely. >> From local host, I use the web-browser to connect to w2web in the >> remote machine, by >> safari http://hostname_where_w2web_runs:7890 >> and open a session successfully. >> However, when I click "view structure" on the left panel, the >> Xcrysden utility is started on the screen >> of the remote host instead of on my local machine. >> One way I can think of: ssh to the remote host and start up >> xcrysden separately and open the structure file. >> However, is there any other way (I mean within w2web) to have >> xcrysden display the picture on the local >> machine? Both of my machines (local and remote) are the Mac OSX >> systems. >> Any help/suggestion would be appreciated. >> Jianxin >> ___ >> Wien mailing list >> Wien at zeus.theochem.tuwien.ac.at >> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > > -- > - > Peter Blaha > Inst. Materials Chemistry, TU Vienna > Getreidemarkt 9, A-1060 Vienna, Austria > Tel: +43-1-5880115671 > Fax: +43-1-5880115698 > email: pblaha at theochem.tuwien.ac.at > - > ___ > Wien mailing list > Wien at zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
[Wien] Parallel calculation with Dual Quad Core Processors
Do you use the serial or the parallel version of the MKL ? The MKL that is used for matrix operations is internally parllelized, the behaviour is usually controlled by the environment variables OMP_NUM_THREADS or MKL_NUM_THREADS as well as some other MKL rlated ones (check the MKL manual). The use of the parallel MKL may therefore cause that all of youre cores are used. Usually the Wien2k config script sets OMP_NUM_THREADS=1 in the bash.rc, If you do not figure out what was setting the thread number for the MKL, try to force that Wien2k uses the serial version (check the compiler and linker options in the Intel manuals) Indeed the use of sveral threads for the mkl and k-point parallelization may be contraproductive and can even slow down the program Note if you change the number of threads using OMP_NUM_THREADS=1, you may need to restart W2WEB, otherwise it stays with the old value. Ciao Gerhard Dr. Gerhard H. Fecher Institut of Inorganic and Analytical Chemistry Johannes Gutenberg - University 55099 Mainz Von: wien-bounces at zeus.theochem.tuwien.ac.at [wien-bounces at zeus.theochem.tuwien.ac.at] im Auftrag von ?? [cma at blem.ac.cn] Gesendet: Sonntag, 10. Januar 2010 00:32 An: wien at zeus.theochem.tuwien.ac.at Betreff: Re: [Wien] Parallel calculation with Dual Quad Core Processors Dear Prof. Marks, Thanks very much for your suggestions. Now, I know how to set up the parallel calculation and edit .machines. In addition, I have another question about the performance of my machine with Dual Quad Core Processors (i. e. 8 CPUs). By checking the process, I found eight CPUs of my machine were all used by more than 90%, even when I performed the calculation without k-point parallelization. I have compared these two cases with and without k-point parallelization, and found that they almost took the same time. So, I think it is not necessary to perform k-point parallel calculation in my case, and that this workstation will automatically allocate the mission on average to all eight CPUs . Is my understanding right? Thanks, Best regards, Chao
[Wien] Running on Teragrid (queenbee.loni-lsu)
Has anyone got anywhere with running Wien2k on the Teragrid (specifically Queenbee). I'm using version 9.1 with ifort 10.1/cmkl and have compiled using both mvapich and mvapich2. So far mvapich "works", but larger lapw1_mpi using 256 cores hang which I cannot get mvapich2 to even run the straight mpi benchmark. N.B., has anyone got mvapich2 and/or mpich2 working with mkl for larger mpi jobs? -- 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/ Electron crystallography is the branch of science that uses electron scattering and imaging to study the structure of matter.
[Wien] optimize.job script for bash shells
The first line of this script calls the csh shell. Hence you can flawlessly execute in on a system that has bash by default (provided csh is available). Stefaan Citeren "Francisco Garcia" : > Dear users, > > I am running simple volume optimization jobs on a shared memory > architecture. > > My shell is a bash shell but the optimize.job script is written for csh > shells. > > Can someone supply me with a bash version of optimize.job? > > (A generic one which allows me to make simple modifications will be fine) > > Thank you. > -- Stefaan Cottenier Center for Molecular Modeling (CMM) Ghent University Technologiepark 903 (2nd floor) BE-9052 ZWIJNAARDE Belgium http://molmod.Ugent.be email: Stefaan.Cottenier /at/ UGent.be
[Wien] Orbital Polarization
Dear users, I would like to know if it makes sense to include orbital polarization in DFT calculations when spin-orbit interaction is absent. Thank you. -- next part -- An HTML attachment was scrubbed... URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20100110/78e8c6e0/attachment.htm>
[Wien] Parallel calculation with Dual Quad Core Processors
Dear Prof. Marks, Thanks very much for your suggestions. Now, I know how to set up the parallel calculation and edit .machines. In addition, I have another question about the performance of my machine with Dual Quad Core Processors (i. e. 8 CPUs). By checking the process, I found eight CPUs of my machine were all used by more than 90%, even when I performed the calculation without k-point parallelization. I have compared these two cases with and without k-point parallelization, and found that they almost took the same time. So, I think it is not necessary to perform k-point parallel calculation in my case, and that this workstation will automatically allocate the mission on average to all eight CPUs . Is my understanding right? Thanks, Best regards, Chao -- next part -- An HTML attachment was scrubbed... URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20100110/86489b71/attachment.htm>
