Re: [Wien] System configuration
Also unable to install ELPA The following might be helpful for those interested in ELPA. ELPA seemed to compile without any problems with the Intel compilers. However, the "make check" tests do not pass for my AMD processor laptop. My hardware resources seem to be lacking that needed for the mpiexec processes of the tests. Perhaps the tests will fair better on a higher end Intel processor system. The Intel Parallel Studio XE 2019 seems like it might be quite buggy up to the current update 4 version, for example the discussion in the Intel forum [ https://software.intel.com/en-us/forums/intel-clusters-and-hpc-technology/topic/799716 ]. So if you encounter issues with 2019, you may want to fallback on an older 2018 version. It might just be due to my particular non-Intel hardware system, but mpiexec.hydra fails with a core dump with Intel Parallel Studio XE 2019 update 4 while it runs using Intel Parallel Studio XE 2018 update 2 for the Hello World mpi demonstration [ https://software.intel.com/en-us/articles/using-intelr-mpi-library-50-with-mpich3-based-applications ]. Building ELPA username@computername:~$ cd ~ username@computername:~$ wget http://elpa.mpcdf.mpg.de/html/Releases/2018.11.001/elpa-2018.11.001.tar.gz ... username@computername:~$ tar xvf elpa-2018.11.001.tar.gz ... username@computername:~$ cd elpa-2018.11.001/ username@computername:~/elpa-2018.11.001$ ./configure FC=mpiifort CC=mpiicc --prefix=$HOME/elpa-2018.11.001 FCFLAGS="-O0 -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -I/opt/intel/compilers_and_libraries_2019.4.243/linux/mkl/include -L/opt/intel/compilers_and_libraries_2019.4.243/linux/mkl/lib/intel64 -lpthread -ldl -liomp5" SCALAPACK_LDFLAGS="-L/opt/intel/compilers_and_libraries_2019.4.243/linux/mkl/lib/intel64 -lmkl_scalapack_lp64 -L/opt/intel/compilers_and_libraries_2019.4.243/linux/mkl/lib/intel64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core" CFLAGS="-O0 -traceback" ... username@computername:~/elpa-2018.11.001$ make ... username@computername:~/elpa-2018.11.001$ make check ... Testsuite summary for elpa 2018.11.001 # TOTAL: 126 # PASS: 0 # SKIP: 45 # XFAIL: 0 # FAIL: 81 # XPASS: 0 # ERROR: 0 ... username@computername:~/elpa-2018.11.001$ make install ... username@computername:~/elpa-2018.11.001$ ls -l ~/elpa-2018.11.001/lib total 4476 -rw-r--r-- 1 username username 2666548 May 28 02:42 libelpa.a -rwxr-xr-x 1 username username 1125 May 28 02:42 libelpa.la lrwxrwxrwx 1 username username 17 May 28 02:42 libelpa.so -> libelpa.so.13.0.0 lrwxrwxrwx 1 username username 17 May 28 02:42 libelpa.so.13 -> libelpa.so.13.0.0 -rwxr-xr-x 1 username username 1903968 May 28 02:42 libelpa.so.13.0.0 drwxr-xr-x 2 username username 4096 May 28 02:42 pkgconfig Intel Parallel Studio XE 2019 update 4 Hello World mpi demo username@computername:~/Desktop/test$ mpiicc -v mpiicc for the Intel(R) MPI Library 2019 Update 4 for Linux* Copyright 2003-2019, Intel Corporation. icc version 19.0.4.243 (gcc version 7.4.0 compatibility) username@computername:~/Desktop/test$ mpiicc ./version_info.c -o version_info username@computername:~/Desktop/test$ mpiexec.hydra -n 2 ./version_info Floating point exception (core dumped) Intel Parallel Studio XE 2018 update 2 Hello World mpi demo username@computername:~/Desktop/test$ mpiicc -v mpiicc for the Intel(R) MPI Library 2018 Update 2 for Linux* Copyright(C) 2003-2018, Intel Corporation. All rights reserved. icc version 18.0.2 (gcc version 7.0.0 compatibility) username@computername:~/Desktop/test$ mpiicc ./version_info.c -o version_info username@computername:~/Desktop/test$ mpiexec.hydra -n 2 ./version_info Hello world: MPI implementation: Intel(R) MPI Library 2018 Update 2 for Linux* OS ___ 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] Issue regarding default iteration (40) in scf calculation during mbj calculation
What I see is run -i120 if this is the case, there is a space missing, it should be run -i 120 Mensaje original De: Indranil mal Fecha: 30/5/19 1:49 PM (GMT-06:00) A: A Mailing list for WIEN2k users Asunto: [Wien] Issue regarding default iteration (40) in scf calculation during mbj calculation Dear users and respected sir, I am trying to calculate band structure of TiC basic unit cell system using mbj potential with a pc with serial compilation. However, every time the SCF iteration stops at 40 cycle then I am compiling "run_lapw -NI -i120" still in the next step it stops after 4o iterations. Please help Thanking you Indranil ___ 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] Issue regarding default iteration (40) in scf calculation during mbj calculation
-i 120 On Thu, May 30, 2019 at 7:56 PM Indranil mal wrote: > Dear users and respected sir, > I am trying to calculate band structure of TiC basic > unit cell system using mbj potential with a pc with serial compilation. > However, every time the SCF iteration stops at 40 cycle then I am compiling > "run_lapw-NI -i120" still in the next step it stops after 4o > iterations. > > Please help > > > Thanking you > > Indranil > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > > https://urldefense.proofpoint.com/v2/url?u=http-3A__zeus.theochem.tuwien.ac.at_mailman_listinfo_wien=DwICAg=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0=WRj445yZoS82Sk4_TpRF_w5R3ecqSPMQqLCGbsM7m7k=v4Lz5bzjZri7S-QOEfniMbgItFNlLGZ2qIBB6ROwhok= > SEARCH the MAILING-LIST at: > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_index.html=DwICAg=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0=WRj445yZoS82Sk4_TpRF_w5R3ecqSPMQqLCGbsM7m7k=68VUZ-8Fi_1H0hb8FeuDkZza8xX5U00BWcL2qj3Goco= > -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu Corrosion in 4D: www.numis.northwestern.edu/MURI 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 ___ 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] Issue regarding default iteration (40) in scf calculation during mbj calculation
Dear users and respected sir, I am trying to calculate band structure of TiC basic unit cell system using mbj potential with a pc with serial compilation. However, every time the SCF iteration stops at 40 cycle then I am compiling "run_lapw-NI -i120" still in the next step it stops after 4o iterations. Please help Thanking you Indranil ___ 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] System configuration
After following the references now getting the following error
> stop error
grep: *scf1*: No such file or directory
cp: cannot stat '.in.tmp': No such file or directory
FERMI - Error
grep: *scf1*: No such file or directory
InBi.scf1_1: No such file or directory.
[1] + Done ( ( $remote $machine[$p] "cd $PWD;$t
$taskset0 $exe ${def}_$loop.def ;fixerror_lapw ${def}_$loop"; rm -f
.lock_$lockfile[$p] ) >& .stdout1_$loop; if ( -f .stdout1_$loop )
bashtime2csh.pl_lapw .stdout1_$loop > .temp1_$loop; grep \% .temp1_$loop >>
.time1_$loop; grep -v \% .temp1_$loop | perl -e "print stderr " )
[2] - Done ( ( $remote $machine[$p] "cd $PWD;$t
$taskset0 $exe ${def}_$loop.def ;fixerror_lapw ${def}_$loop"; rm -f
.lock_$lockfile[$p] ) >& .stdout1_$loop; if ( -f .stdout1_$loop )
bashtime2csh.pl_lapw .stdout1_$loop > .temp1_$loop; grep \% .temp1_$loop >>
.time1_$loop; grep -v \% .temp1_$loop | perl -e "print stderr " )
bash: fixerror_lapw: command not found
bash: lapw1c: command not found
bash: fixerror_lapw: command not found
bash: lapw1c: command not found
LAPW0 END
LAPW0 END
On Thu, May 30, 2019 at 10:22 AM Gavin Abo wrote:
> Refer to [1,2], you may need to install the operating system's ssh-askpass
> package or setup passwordless login with ssh-keygen [3] and ssh-copy-id [4].
>
> [1]
> https://stackoverflow.com/questions/10050556/setting-up-ssh-for-jenkins-to-use-at-runtime
> [2]
> https://askubuntu.com/questions/45679/ssh-connection-problem-with-host-key-verification-failed-error
> [3]
> https://www.tecmint.com/ssh-passwordless-login-using-ssh-keygen-in-5-easy-steps/
> [4] https://www.ssh.com/ssh/copy-id
>
> On 5/29/2019 9:52 PM, Indranil mal wrote:
>
> compiled fftw with intel mpi and successfully compiled without any error.
> After running a job in parallel scf GOT THE FOLLOWING ERROR
>
> grep: *scf1*: No such file or directory
> cp: cannot stat '.in.tmp': No such file or directory
> FERMI - Error
> grep: *scf1*: No such file or directory
> InBi.scf1_1: No such file or directory.
> [1] + Done ( ( $remote $machine[$p] "cd $PWD;$t
> $taskset0 $exe ${def}_$loop.def ;fixerror_lapw ${def}_$loop"; rm -f
> .lock_$lockfile[$p] ) >& .stdout1_$loop; if ( -f .stdout1_$loop )
> bashtime2csh.pl_lapw .stdout1_$loop > .temp1_$loop; grep \% .temp1_$loop >>
> .time1_$loop; grep -v \% .temp1_$loop | perl -e "print stderr " )
> Host key verification failed.
> ssh_askpass: exec(/usr/bin/ssh-askpass): No such file or directory
> [1] + Done ( ( $remote $machine[$p] "cd $PWD;$t
> $taskset0 $exe ${def}_$loop.def ;fixerror_lapw ${def}_$loop"; rm -f
> .lock_$lockfile[$p] ) >& .stdout1_$loop; if ( -f .stdout1_$loop )
> bashtime2csh.pl_lapw .stdout1_$loop > .temp1_$loop; grep \% .temp1_$loop >>
> .time1_$loop; grep -v \% .temp1_$loop | perl -e "print stderr " )
> Host key verification failed.
> ssh_askpass: exec(/usr/bin/ssh-askpass): No such file or directory
> LAPW0 END
> LAPW0 END
>
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Re: [Wien] Structural phase transition
I forgot to the link of the paper. https://iopscience.iop.org/article/10.1088/1674-1056/18/1/043 On Thu, May 30, 2019 at 10:10 AM Subhasis Panda wrote: > Thank you, Sir, for the help! > I'm still having some doubts. > For studying the structural phase transition at T=0K, I've plotted > enthalpy against pressure and got the transition pressure (T_p) from Gibbs2 > data which is similar to the one mentioned in the attached paper. > Gibbs2 under QHA (Debye-Slater model) provides G by varying p and T at a > prescribed interval. When I plot \deltaG =0 I got many (p,T) points, when > plotted I get the temperature variation of the transition pressure (T_p). > > But I am not getting the transition temperature as mentioned in figure 3 > of the attached paper at P=0Gpa. > The Entropy calculated in Gibbs2 can it be used for this study? > > > > On Wed, May 29, 2019, 5:55 PM Peter Blaha > wrote: > >> Finite temperature requires the entropy. So you would not compare >> enthalpies, but free energies. >> The main contribution to the entropy comes from the phonons. Thus you >> must calculate the phonons and from the corresponding phonon-DOS you can >> get the "-TS" contribution to the free energy. >> >> Phonons can be calculated with WIEN2k and the help of programs like >> PHONOPY or PHONON (see unsupported software at www.wien2k.at) and one >> would do what is called the "quasiharmonic" approximation (i.e. >> calculate the phonons at various volumes). >> This is straight forward and has been done many times in Literature. >> >> However, this approach fails eventually, since in the harmonic >> approximation some phonons might be instable, giving imaginary >> frequencies. >> >> In that case, anharmonic terms are needed and several different schemes >> are discussed in Literature without consensus about the best method. In >> any case, all these calculations become very expensive. >> >> On 5/18/19 8:57 PM, Subhasis Panda wrote: >> > Dear experts, >> > I've used Wien2k and subsequently Gibbs2 package to study structural >> > phase transition between two polymorphs of a material. The enthalpy vs >> > pressure plot at T=0K gives me the transition pressure for a particular >> > transition. >> > However, when I try to plot difference of Gibbs free energy at P=0 GPa >> > it doesn't cross zero. But, the literature is showing transition >> > temperature for the phase transition. >> > So, my questions are >> > 1) How to determine the transition temperature at P=0 GPa or at any >> > pressure? >> > 2) How do we get the variation of transition pressure with temperature? >> > Looking forward for your valuable comments. >> > Any reference in this direction is most welcomed. >> > Thank you in advance for the help. >> > >> > ___ >> > 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 >> > >> >> -- >> >>P.Blaha >> -- >> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna >> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 >> Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at >> WWW: http://www.imc.tuwien.ac.at/TC_Blaha >> -- >> ___ >> 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 >> > -- Best regards, Subhasis Panda Assistant Professor Department of Physics National Institute of Technology Silchar Assam, India - 788010. - ___ 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
