[Wien] Regarding the electronic properties of band gap of super cell
Hello everyone We are trying to calculate electronic properties of super cell structures for a specific doping percentages. Where the unit cell is from zinc blend space group with four atoms each anion and cation total 8 atoms for and a doping concentration of 6.25%. We have tried with two different supper cell 1. Incorporated 2 impurity atom in p type 2x2x2 supper cell consist of 32 atoms each anion and cation and total 64 atoms. [(2*100/32)=6.25] 2. Incorporated 1 impurity atom in p type 1x2x2 supper cell consist of 16 atoms each anion and cation and total 32 atoms. [(1*100/16)=6.25] For both the cases we have considered the same ec cc fc for convergence and same XC and mBJ potential and same numbers of k points. The structural properties are more or less same for both the case. However, the the electronic properties are not same for the cases. It will be helpful if you kindly suggest us for corrections to get same result. We have constrain in computation resources and that is why we want to compute greater impurity percentage with smaller supper cell structures. 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] parallel ssh error
Thank you Sir for your instantaneous support. Now it is working smoothly only with hup: Command not found. On Sun, Sep 29, 2019 at 6:32 PM Gavin Abo wrote: > Checking with "which lapw1c" on each node (vlsi1, vlsi2, vlsi3, and vlsi4) > is a good idea. However, since WIENROOT is (blank) [1], it probably won't > work until that is resolved. > > It was mentioned that the WIEN2k .bashrc block was setup on each node by > running userconfig [2]. So it definitely seems strange that WIENROOT is > (blank) on the client nodes since I would think it would work if both > WIENROOT and PATH are both defined from userconfig in .bashrc: > > username@computername:~$ ssh vlsi1 > ... > username@computername:~$ cd ~/WIEN2k > username@computername:~/WIEN2k$ which lapw1c > username@computername:~/WIEN2k$ grep "export WIENROOT" ~/.bashrc > username@computername:~/WIEN2k$ grep "export PATH" ~/.bashrc > username@computername:~/WIEN2k$ ./userconfig > ... > username@computername:~/WIEN2k$ grep "export WIENROOT" ~/.bashrc > export WIENROOT=/servernode1 > username@computername:~/WIEN2k$ grep "export PATH" ~/.bashrc > export > PATH=$WIENROOT:$STRUCTEDIT_PATH:$WIENROOT/SRC_IRelast/script-elastic:$PATH:. > export PATH=$PATH:$WIENROOT:. > username@computername:~/WIEN2k$ source ~/.bashrc > username@computername:~/WIEN2k$ which lapw1c > /home/username/WIEN2k/lapw1c > username@computername:~/WIEN2k$ exit > logout > Connection to vlsi1 closed. > > Though, I suppose if something like a conf file [3] was setup by the user > to override .bashrc or a job queue scheduler system is in use [4] it might > also cause the issue. > [1] > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19052.html > [2] > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19036.html > [3] > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08016.html > [4] > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15985.html > > On 9/29/2019 6:11 AM, Laurence Marks wrote: > > What does > > ssh vlsi1 which lapw1c > give, what does "cat *.error" give in the case directory? > _ > Professor Laurence Marks > "Research is to see what everybody else has seen, and to think what nobody > else has thought", Albert Szent-Gyorgi > www.numis.northwestern.edu > > On Sun, Sep 29, 2019, 01:17 Indranil mal wrote: > >> Now echo $WIENROOT is giving the $WIENROOT location. >> >> echo $WIENROOT/lapw* >> >> /home/username/WIEN2K/lapw0 /home/username/WIEN2K/lapw0_mpi >> /home/username/WIEN2K/lapw0para /home/username/WIEN2K/lapw0para_lapw >> /home/username/WIEN2K/lapw1 /home/username/WIEN2K/lapw1c >> /home/username/WIEN2K/lapw1c_mpi /home/username/WIEN2K/lapw1cpara >> /home/username/WIEN2K/lapw1_mpi /home/username/WIEN2K/lapw1para >> /home/username/WIEN2K/lapw1para_lapw /home/username/WIEN2K/lapw2 >> /home/username/WIEN2K/lapw2c /home/username/WIEN2K/lapw2c_mpi >> /home/username/WIEN2K/lapw2cpara /home/username/WIEN2K/lapw2_mpi >> /home/username/WIEN2K/lapw2para /home/username/WIEN2K/lapw2para_lapw >> /home/username/WIEN2K/lapw3 /home/username/WIEN2K/lapw3c >> /home/username/WIEN2K/lapw5 /home/username/WIEN2K/lapw5c >> /home/username/WIEN2K/lapw7 /home/username/WIEN2K/lapw7c >> /home/username/WIEN2K/lapwdm /home/username/WIEN2K/lapwdmc >> /home/username/WIEN2K/lapwdmcpara /home/username/WIEN2K/lapwdmpara >> /home/username/WIEN2K/lapwdmpara_lapw /home/username/WIEN2K/lapwso >> /home/username/WIEN2K/lapwsocpara /home/username/WIEN2K/lapwso_mpi >> /home/username/WIEN2K/lapwsopara /home/username/WIEN2K/lapwsopara_lapw >> >> ssh vlsi1 'echo $WIENROOT/lapw*' >> >> /home/username/WIEN2K/lapw0 /home/username/WIEN2K/lapw0_mpi >> /home/username/WIEN2K/lapw0para /home/username/WIEN2K/lapw0para_lapw >> /home/username/WIEN2K/lapw1 /home/username/WIEN2K/lapw1c >> /home/username/WIEN2K/lapw1c_mpi /home/username/WIEN2K/lapw1cpara >> /home/username/WIEN2K/lapw1_mpi /home/username/WIEN2K/lapw1para >> /home/username/WIEN2K/lapw1para_lapw /home/username/WIEN2K/lapw2 >> /home/username/WIEN2K/lapw2c /home/username/WIEN2K/lapw2c_mpi >> /home/username/WIEN2K/lapw2cpara /home/username/WIEN2K/lapw2_mpi >> /home/username/WIEN2K/lapw2para /home/username/WIEN2K/lapw2para_lapw >> /home/username/WIEN2K/lapw3 /home/username/WIEN2K/lapw3c >> /home/username/WIEN2K/lapw5 /home/username/WIEN2K/lapw5c >> /home/username/WIEN2K/lapw7 /home/username/WIEN2K/lapw7c >> /home/username/WIEN2K/lapwdm /home/username/WIEN2K/lapwdmc >> /home/username/WIEN2K/lapwdmcpara /home/username/WIEN2K/lapwdmpara >> /home/user
Re: [Wien] parallel ssh error
Now echo $WIENROOT is giving the $WIENROOT location. echo $WIENROOT/lapw* /home/username/WIEN2K/lapw0 /home/username/WIEN2K/lapw0_mpi /home/username/WIEN2K/lapw0para /home/username/WIEN2K/lapw0para_lapw /home/username/WIEN2K/lapw1 /home/username/WIEN2K/lapw1c /home/username/WIEN2K/lapw1c_mpi /home/username/WIEN2K/lapw1cpara /home/username/WIEN2K/lapw1_mpi /home/username/WIEN2K/lapw1para /home/username/WIEN2K/lapw1para_lapw /home/username/WIEN2K/lapw2 /home/username/WIEN2K/lapw2c /home/username/WIEN2K/lapw2c_mpi /home/username/WIEN2K/lapw2cpara /home/username/WIEN2K/lapw2_mpi /home/username/WIEN2K/lapw2para /home/username/WIEN2K/lapw2para_lapw /home/username/WIEN2K/lapw3 /home/username/WIEN2K/lapw3c /home/username/WIEN2K/lapw5 /home/username/WIEN2K/lapw5c /home/username/WIEN2K/lapw7 /home/username/WIEN2K/lapw7c /home/username/WIEN2K/lapwdm /home/username/WIEN2K/lapwdmc /home/username/WIEN2K/lapwdmcpara /home/username/WIEN2K/lapwdmpara /home/username/WIEN2K/lapwdmpara_lapw /home/username/WIEN2K/lapwso /home/username/WIEN2K/lapwsocpara /home/username/WIEN2K/lapwso_mpi /home/username/WIEN2K/lapwsopara /home/username/WIEN2K/lapwsopara_lapw ssh vlsi1 'echo $WIENROOT/lapw*' /home/username/WIEN2K/lapw0 /home/username/WIEN2K/lapw0_mpi /home/username/WIEN2K/lapw0para /home/username/WIEN2K/lapw0para_lapw /home/username/WIEN2K/lapw1 /home/username/WIEN2K/lapw1c /home/username/WIEN2K/lapw1c_mpi /home/username/WIEN2K/lapw1cpara /home/username/WIEN2K/lapw1_mpi /home/username/WIEN2K/lapw1para /home/username/WIEN2K/lapw1para_lapw /home/username/WIEN2K/lapw2 /home/username/WIEN2K/lapw2c /home/username/WIEN2K/lapw2c_mpi /home/username/WIEN2K/lapw2cpara /home/username/WIEN2K/lapw2_mpi /home/username/WIEN2K/lapw2para /home/username/WIEN2K/lapw2para_lapw /home/username/WIEN2K/lapw3 /home/username/WIEN2K/lapw3c /home/username/WIEN2K/lapw5 /home/username/WIEN2K/lapw5c /home/username/WIEN2K/lapw7 /home/username/WIEN2K/lapw7c /home/username/WIEN2K/lapwdm /home/username/WIEN2K/lapwdmc /home/username/WIEN2K/lapwdmcpara /home/username/WIEN2K/lapwdmpara /home/username/WIEN2K/lapwdmpara_lapw /home/username/WIEN2K/lapwso /home/username/WIEN2K/lapwsocpara /home/username/WIEN2K/lapwso_mpi /home/username/WIEN2K/lapwsopara /home/username/WIEN2K/lapwsopara_lapw However getting the same 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 Parallel.scf1_1: No such file or directory. bash: fixerror_lapw: command not found bash: lapw1c: command not found bash: fixerror_lapw: command not found bash: lapw1c: command not found bash: fixerror_lapw: command not found bash: lapw1c: command not found bash: fixerror_lapw: command not found bash: lapw1c: command not found bash: fixerror_lapw: command not found bash: lapw1c: command not found bash: fixerror_lapw: command not found bash: lapw1c: command not found LAPW0 END hup: Command not found. and lapw2 error file 'LAPW2' - can't open unit: 30 'LAPW2' -filename: Parallel.energy_1 ** testerror: Error in Parallel LAPW2 On Sat, Sep 28, 2019 at 11:58 PM Gavin Abo wrote: > The "sudo service sshd restart" step, which I forgot to copy and paste, > that is missing is corrected below. > On 9/28/2019 12:18 PM, Gavin Abo wrote: > > After you set both "SendEnv *" and "AcceptEnv *", did you restart the sshd > service [1]? The following illustrates steps that might help you verify > that WIENROOT appears on a remote vlsi node: > > username@computername:~$ echo $WIENROOT > > username@computername:~$ export WIENROOT=/servernode1 > username@computername:~$ echo $WIENROOT > /servernode1 > username@computername:~$ ssh vlsi > Welcome to Ubuntu 18.04.3 LTS (GNU/Linux 4.15.0-64-generic x86_64) > ... > Last login: Sat Sep 28 12:04:07 2019 from xxx.x.x.x > username@computername:~$ echo $WIENROOT > > username@computername:~$ exit > logout > Connection to vlsi closed. > username@computername:~$ sudo gedit /etc/ssh/ssh_config > [sudo] password for username: > > username@computername:~$ sudo gedit /etc/ssh/sshd_config > > username@computername:~$ grep SendEnv /etc/ssh/ssh_config > SendEnv LANG LC_* WIENROOT > username@computername:~$ grep AcceptEnv /etc/ssh/sshd_config > AcceptEnv LANG LC_* WIENROOT > >username@computername:~$ sudo service sshd restart > > username@computername:~$ ssh vlsi > ... > username@computername:~$ echo $WIENROOT > /servernode1 > username@computername:~$ exit > > [1] > https://askubuntu.com/questions/462968/take-changes-in-file-sshd-config-file-without-server-reboot > On 9/28/2019 11:22 AM, Indranil mal wrote: > > Sir I have tried with " SetEnv * " Still nothing is coming with echo > commad and user name by mistake I posted wrong Otherwise no issue with > user name and I
Re: [Wien] parallel ssh error
Sir I have tried with " SetEnv * " Still nothing is coming with echo commad and user name by mistake I posted wrong Otherwise no issue with user name and I have set the parallel options file taksset "no" and remote options are 1 1 in server and client machines. On Sat, 28 Sep 2019 11:36 Gavin Abo, wrote: > Respected Sir, In my linux(Ubuntu 18.04 LTS) in ssh_config, and in > sshd_config there are two line already "SendEnv LANG LC_*" "AcceptEnv LANG > LC_*" respectively. > > The "LANG LC_*" probably only puts just the local language variables in > the remote environment. Did you follow the previous advice [1] of trying > to use "*" to put all variables from the local environment? > > [1] > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19049.html > > However, ssh vsli1 'echo $WIENROOT' gives nothing (blank). > > That seems to be the main cause of the problem as it should not return > (blank) but needs to return "/servernode1" as you previously mentioned [2]. > > [2] > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19036.html > > Perhaps the message below is a clue. It you had set the WIENROOT variable > in .bashrc of your /home/vlsi accounts on each system, you likely have to > login and use that same /home/vlsi account on the head node as the output > below seems to indicate login to a different /home/niel account. > Alternatively, setting the WIENROOT variable in .bashrc of all /home/niel > accounts on each node might work too. > >The command ssh vsli1 'pwd $WIENROOT' print "/home/vlsi" the common > home directory and > ssh vlsi1 "env" > ... > USER=niel > PWD=/home/niel > HOME=/home/niel > ... > this is similar as server, and other nodes. > > Sir After changing the parallel option file in $WIENROOT in server to > > setenv TASKSET *"yes" from "no"* > if ( ! $?USE_REMOTE ) setenv USE_REMOTE 1 > if ( ! $?MPI_REMOTE ) setenv MPI_REMOTE 1 > setenv WIEN_GRANULARITY 1 > setenv DELAY 0.1 > setenv SLEEPY 1 > setenv WIEN_MPIRUN "mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_" > setenv CORES_PER_NODE 1 > > the error is not coming but the program is not increasing steps after > lapw0 it stuck in lapw1 > > Since it seemed to be throwing an appropriate error message with TASKSET > previously unlike when set to "yes", probably you should change it back to > "no". > ___ > 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] parallel ssh error
Respected Sir, In my linux(Ubuntu 18.04 LTS) in ssh_config, and in sshd_config there are two line already "SendEnv LANG LC_*" "AcceptEnv LANG LC_*" respectively. However, ssh vsli1 'echo $WIENROOT' gives nothing (blank). The command ssh vsli1 'pwd $WIENROOT' print "/home/vlsi" the common home directory and ssh vlsi1 "env" SSH_CONNECTION=172.27.46.251 44138 172.27.46.233 22 LANG=en_IN XDG_SESSION_ID=47 USER=niel PWD=/home/niel HOME=/home/niel SSH_CLIENT=172.27.46.251 44138 22 LC_NUMERIC=POSIX MAIL=/var/mail/niel SHELL=/bin/bash SHLVL=1 LANGUAGE=en_IN:en LOGNAME=niel DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1000/bus XDG_RUNTIME_DIR=/run/user/1000 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games _=/usr/bin/env this is similar as server, and other nodes. Sir After changing the parallel option file in $WIENROOT in server to setenv TASKSET *"yes" from "no"* if ( ! $?USE_REMOTE ) setenv USE_REMOTE 1 if ( ! $?MPI_REMOTE ) setenv MPI_REMOTE 1 setenv WIEN_GRANULARITY 1 setenv DELAY 0.1 setenv SLEEPY 1 setenv WIEN_MPIRUN "mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_" setenv CORES_PER_NODE 1 the error is not coming but the program is not increasing steps after lapw0 it stuck in lapw1 what should be the parallel option file in server and all client node? On Fri, Sep 27, 2019 at 12:05 PM Peter Blaha wrote: > Ok. So the problem seems to be that in your linux the ssh does not > send/accept the "environment". > > What do you get with: > > ssh vsli2 'echo $WIENROOT' > > If you have root permissions, I suggest to do the following: > > At least on my Linux (Suse) there is a /etc/ssh directory, with files > > ssh_config and sshd_config. > > Edit these files and add lines: > SendEnv * # in ssh_config > AcceptEnv *# in sshd_config > > > > On 9/27/19 11:20 AM, Indranil mal wrote: > > Respected Sir, As per Your suggestion I have done the single process > > with one iteration successfully encountered no issue in all the nodes. > > However in parallel running facing the same 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 > > Parallel.scf1_1: No such file or directory. > > bash: fixerror_lapw: command not found > > bash: lapw1c: command not found > > bash: fixerror_lapw: command not found > > bash: lapw1c: command not found > > bash: fixerror_lapw: command not found > > bash: lapw1c: command not found > > bash: fixerror_lapw: command not found > > bash: lapw1c: command not found > > bash: fixerror_lapw: command not found > > bash: lapw1c: command not found > > bash: fixerror_lapw: command not found > > bash: lapw1c: command not found > > bash: fixerror_lapw: command not found > > bash: lapw1c: command not found > > bash: fixerror_lapw: command not found > > bash: lapw1c: command not found > > LAPW0 END > > hup: Command not found. > > > > Previously I was doing a mistake with user name and home directory now > in all the pc the user name and the home directory is same (/home/vlsi) is > same and the working directory is accessible from every node. > > > > (ls -l $WIENROOT/lapw1c > > -rwxr-xr-x 1 vlsi vlsi 2151824 Sep 26 02:41 /servernode01/lapw1c) this > reflects in all the pcs. > > > > > > > > > > On Thu, Sep 26, 2019 at 1:27 PM Peter Blaha > > mailto:pbl...@theochem.tuwien.ac.at>> > wrote: > > > > First of all, one of the errors was: lapw1c: command not found > > > > You showed us only the existence of "lapw1", not "lapw1c" with the ls > > commands. > > > > However, since you also have: fixerror_lapw: command not found > > > > I don't think that this is the problem. > > > > - > > I'm more concerned about the different usernames/owners of lapw1 on > > different computers. > > It is not important who owns $WIENROOT/*, as long as everybody has > r-x > > permissions. > > > > However, what is your username and your home-directory on the > different > > machines ? It must be the same ! And do you have access to the actual > > working directory ? > > In what directory did you start the calculations? > > Is it a directory called "Parallel" ? What is the full path of that > on > > every computer (/casenode1/Parallel ?) > > -- > > > > First check would be: > > > &
Re: [Wien] parallel ssh error
Respected Sir, As per Your suggestion I have done the single process with
one iteration successfully encountered no issue in all the nodes. However
in parallel running facing the same 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
Parallel.scf1_1: No such file or directory.
bash: fixerror_lapw: command not found
bash: lapw1c: command not found
bash: fixerror_lapw: command not found
bash: lapw1c: command not found
bash: fixerror_lapw: command not found
bash: lapw1c: command not found
bash: fixerror_lapw: command not found
bash: lapw1c: command not found
bash: fixerror_lapw: command not found
bash: lapw1c: command not found
bash: fixerror_lapw: command not found
bash: lapw1c: command not found
bash: fixerror_lapw: command not found
bash: lapw1c: command not found
bash: fixerror_lapw: command not found
bash: lapw1c: command not found
LAPW0 END
hup: Command not found.
Previously I was doing a mistake with user name and home directory now
in all the pc the user name and the home directory is same
(/home/vlsi) is same and the working directory is accessible from
every node.
(ls -l $WIENROOT/lapw1c
-rwxr-xr-x 1 vlsi vlsi 2151824 Sep 26 02:41 /servernode01/lapw1c) this
reflects in all the pcs.
On Thu, Sep 26, 2019 at 1:27 PM Peter Blaha
wrote:
> First of all, one of the errors was: lapw1c: command not found
>
> You showed us only the existence of "lapw1", not "lapw1c" with the ls
> commands.
>
> However, since you also have: fixerror_lapw: command not found
>
> I don't think that this is the problem.
>
> -
> I'm more concerned about the different usernames/owners of lapw1 on
> different computers.
> It is not important who owns $WIENROOT/*, as long as everybody has r-x
> permissions.
>
> However, what is your username and your home-directory on the different
> machines ? It must be the same ! And do you have access to the actual
> working directory ?
> In what directory did you start the calculations?
> Is it a directory called "Parallel" ? What is the full path of that on
> every computer (/casenode1/Parallel ?)
> --
>
> First check would be:
>
> On vlsi1 change into the working directory (Parallel ?) and run one
> iteration without parallelization: run -i 1
>
> then login to ssh vsli2 (passwordless), cd into "Parallel" and do
> another non-parallel cycle. Does it work ?
> ---
>
>
> On 9/26/19 11:48 AM, Indranil mal wrote:
> > Dear developers and users
> > I have 5 individual Linux
> > (Ubuntu) pc with intel i7 octa core processors and 16GB RAM in each
> > connected via a 1GBps LAN. password less ssh working properly. I have
> > installed WIEN2K 19 in the one machine (M1 server) in the directory
> > "/servernode1" and the case directory is "/casenode1" and through NFS I
> > have mounted the "servernode1", and "casenode1" in other four pcs with
> > same name local folders ("servernode1", and "casenode1") in them. I have
> > installed ,intel compilers, libxc, fftw, elpa in all the nodes
> > individually. I have manually edited the bash file $WIENROOT path and
> > case directory and the WIEN2K options file. Keep all the value same in
> > all the client nodes as it is in the server node.
> >
> > alias cdw="cd /casenode1"
> > export OMP_NUM_THREADS=4
> > #export LD_LIBRARY_PATH=.
> > export EDITOR="emacs"
> > export SCRATCH=./
> > export WIENROOT=/servernode1
> > export W2WEB_CASE_BASEDIR=/casenode1
> > export STRUCTEDIT_PATH=$WIENROOT/SRC_structeditor/bin
> >
> > Now when I am doing parallel calculations with all the client nodes in
> > machine file ,
> > # k-points are left, they will be distributed to the
> residual-machine_name.
> > #
> > 1:vlsi1
> > 1:vlsi2
> > 1:vlsi3
> > 1:vlsi4
> >
> > granularity:1
> > extrafine:1
> > #
> >
> >
> > and getting 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
> > Parallel.scf1_1: No such file or directory.
> > bash: fixerror_lapw: command not found
> > bash: lapw1c: command not found
> > bash: fixerror_lapw: command not found
> > bash: lapw1c: command not found
> > LAPW0 END
> > hup: Command not found.
> >
> > ###Error file lapw2 error
> > 'LAPW2' - can't open unit: 30
> > 'LAPW
[Wien] parallel ssh error
Dear developers and users
I have 5 individual Linux (Ubuntu)
pc with intel i7 octa core processors and 16GB RAM in each connected via a
1GBps LAN. password less ssh working properly. I have installed WIEN2K 19
in the one machine (M1 server) in the directory "/servernode1" and the case
directory is "/casenode1" and through NFS I have mounted the
"servernode1", and "casenode1" in other four pcs with same name local
folders ("servernode1", and "casenode1") in them. I have installed ,intel
compilers, libxc, fftw, elpa in all the nodes individually. I have manually
edited the bash file $WIENROOT path and case directory and the WIEN2K
options file. Keep all the value same in all the client nodes as it is in
the server node.
alias cdw="cd /casenode1"
export OMP_NUM_THREADS=4
#export LD_LIBRARY_PATH=.
export EDITOR="emacs"
export SCRATCH=./
export WIENROOT=/servernode1
export W2WEB_CASE_BASEDIR=/casenode1
export STRUCTEDIT_PATH=$WIENROOT/SRC_structeditor/bin
Now when I am doing parallel calculations with all the client nodes in
machine file ,
# k-points are left, they will be distributed to the residual-machine_name.
#
1:vlsi1
1:vlsi2
1:vlsi3
1:vlsi4
granularity:1
extrafine:1
#
and getting 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
Parallel.scf1_1: No such file or directory.
bash: fixerror_lapw: command not found
bash: lapw1c: command not found
bash: fixerror_lapw: command not found
bash: lapw1c: command not found
LAPW0 END
hup: Command not found.
###Error file lapw2 error
'LAPW2' - can't open unit: 30
'LAPW2' -filename: Parallel.energy_1
** testerror: Error in Parallel LAPW2
I have checked the with " ls -l $WIENROOT/lapw1" as suggested in the
previous mailing list and got the
-rwxr-xr-x 1 vlsi vlsi 2139552 Sep 26 02:41 /servernode1/lapw1 for server
(vlsi is the user name in server)
-rwxr-xr-x 1 vlsi1 vlsi1 2139552 Sep 26 02:41 /servernode1/lapw1 (in node1
the user name is vlsi1)
-rwxr-xr-x 1 vlsi2 vlsi2 2139552 Sep 26 02:41 /servernode1/lapw1 (in node2
the user name is vlsi2)
please help
thanking you
Indranil
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Re: [Wien] IRELAST issue
The solution is given by the author of IRELAST ( Morteza Jamal ) "Please move (not copy) initIR_lapw from SRC_IRelast/script-elastic to WIEN2k directory and then run it again." Now it is working fine. On Sat, Jul 6, 2019 at 4:09 AM Indranil mal wrote: > Dear sir and users, > I am trying to calculate the pressure dependent > elastic constant by following the instruction given in the user guide using > IRELAST in my pc with WIEN2K 18 version. > Unfortunately I am getting the following error while calling the > ./CUBIC.job after setting up the lapw > > # > next is nn > /home/dps/WIENDPS/SRC_IRelast/script-elastic/x: Command not found. > \n stop error \n > clmextrapol_lapw did not extrapolate new density because of missing > test.rsp > head: cannot open 'test.inm' for reading: No such file or directory > head: cannot open 'test.inm' for reading: No such file or directory > no test.clmsum(_old) file found, which is necessary for lapw0 ! > grep: *scf1*: No such file or directory > grep: lapw2*.error: No such file or directory > > > stop error > - > > ERROR status in Styp1_-2.0 > > - > *** > Styp3_-2.0 > *** > > I have tried with the given structure in the example MgO in the > SRC_IRelast folder the same error I am getting. > please 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
[Wien] IRELAST issue
Dear sir and users, I am trying to calculate the pressure dependent elastic constant by following the instruction given in the user guide using IRELAST in my pc with WIEN2K 18 version. Unfortunately I am getting the following error while calling the ./CUBIC.job after setting up the lapw # next is nn /home/dps/WIENDPS/SRC_IRelast/script-elastic/x: Command not found. \n stop error \n clmextrapol_lapw did not extrapolate new density because of missing test.rsp head: cannot open 'test.inm' for reading: No such file or directory head: cannot open 'test.inm' for reading: No such file or directory no test.clmsum(_old) file found, which is necessary for lapw0 ! grep: *scf1*: No such file or directory grep: lapw2*.error: No such file or directory > stop error - ERROR status in Styp1_-2.0 - *** Styp3_-2.0 *** I have tried with the given structure in the example MgO in the SRC_IRelast folder the same error I am getting. please 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
[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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> 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
>
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Re: [Wien] System configuration
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
On Thu, May 30, 2019 at 6:29 AM Gavin Abo wrote:
> As mentioned in a previous post [1], it looks like ompi_mpi in the error
> messages indicate that your fftw3 was compiled with Open MPI instead of
> Intel MPI.
>
> If you have both Open MPI and Intel MPI on your system, you have to take
> care of the double ii's.
>
> Perhaps, you used mpicc for Open MPI [2] instead of mpiicc for Intel MPI
> [3] when you compiled fftw3 [4].
> [1]
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13360.html
> [2] https://www.open-mpi.org/faq/?category=mpi-apps#general-build
> [3]
> https://software.intel.com/en-us/mpi-developer-guide-linux-compilers-support
> [4]
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18664.html
>
>
> On 5/29/2019 11:25 AM, Indranil mal wrote:
>
> /home/dps/fftw3/lib/libfftw3_mpi.a(api.o): In function `bogosity_hook':
> api.c:(.text+0x20): undefined reference to `ompi_mpi_comm_null'
> api.c:(.text+0x44): undefined reference to `ompi_mpi_comm_null'
> api.c:(.text+0x73): undefined reference to `ompi_mpi_comm_null'
> /home/dps/fftw3/lib/libfftw3_mpi.a(api.o): In function `nowisdom_hook':
> api.c:(.text+0x9d): undefined reference to `ompi_mpi_comm_null'
> api.c:(.text+0xbc): undefined reference to `ompi_mpi_comm_null'
> /home/dps/fftw3/lib/libfftw3_mpi.a(api.o):api.c:(.text+0xd3): more
> undefined references to `ompi_mpi_comm_null' follow
> /home/dps/fftw3/lib/libfftw3_mpi.a(api.o): In function `wisdom_ok_hook':
> api.c:(.text+0x1cc): undefined reference to `ompi_mpi_unsigned'
> api.c:(.text+0x21f): undefined reference to `ompi_mpi_op_land'
> api.c:(.text+0x226): undefined reference to `ompi_mpi_int'
> api.c:(.text+0x24b): undefined reference to `ompi_mpi_comm_null'
> /home/dps/fftw3/lib/libfftw3_mpi.a(api.o): In function `cost_hook':
> api.c:(.text+0x2c7): undefined reference to `ompi_mpi_comm_null'
> api.c:(.text+0x2dc): undefined reference to `ompi_mpi_comm_null'
> api.c:(.text+0x2ee): undefined reference to `ompi_mpi_op_max'
> api.c:(.text+0x2f5): undefined reference to `ompi_mpi_op_sum'
> api.c:(.text+0x308): undefined reference to `ompi_mpi_double'
> api.c:(.text+0x33b): undefined reference to `ompi_mpi_comm_null'
> /home/dps/fftw3/lib/libfftw3_mpi.a(f03-wrap.o): In function
> `fftw_mpi_local_size_many_transposed_f03':
> f03-wrap.c:(.text+0x3a): undefined reference to `MPI_Comm_f2c'
> /home/dps/fftw3/lib/libfftw3_mpi.a(f03-wrap.o): In function
> `fftw_mpi_local_size_many_f03':
> f03-wrap.c:(.text+0xa5): undefined reference to `MPI_Comm_f2c'
> /home/dps/fftw3/lib/libfftw3_mpi.a(f03-wrap.o): In function
> `fftw_mpi_local_size_transposed_f03':
> f03-wrap.c:(.text+0x103): undefined reference to `MPI_Comm_f2c'
> /home/dps/fftw3/lib/libfftw3_mpi.a(f03-wrap.o): In function
> `fftw_mpi_local_size_f03':
> f03-wrap.c:(.text+0x148): undefined reference to `MPI_Comm_f2c'
> /home/dps/fftw3/lib/libfftw3_mpi.a(f03-wrap.o): In function
> `fftw_mpi_local_size_many_1d_f03':
> f03-wrap.c:(.text+0x1a2): undefined reference to `MPI_Comm_f2c'
> /home/dps/fftw3/lib/libfftw3_mpi.a(f03-wrap.o):f03-wrap.c:(.text+0x20a):
> more undefined references to `MPI_Comm_f2c' follow
> /home/dps/fftw3/lib/libfftw3_mpi.a(transpose-alltoall.o): In function
> `apply':
> transpose-alltoall.c:(.text+0x83): undefined reference to `ompi_mpi_double'
> transpose-alltoall.c:(.text+0x11f): undefined reference to
> `ompi_mpi_double'
> transpose-alltoall.c:(.text+0x16d): undefined reference to
> `ompi_mpi_double'
> trans
Re: [Wien] System configuration
/home/dps/fftw3/lib/libfftw3_mpi.a(api.o): In function `bogosity_hook': api.c:(.text+0x20): undefined reference to `ompi_mpi_comm_null' api.c:(.text+0x44): undefined reference to `ompi_mpi_comm_null' api.c:(.text+0x73): undefined reference to `ompi_mpi_comm_null' /home/dps/fftw3/lib/libfftw3_mpi.a(api.o): In function `nowisdom_hook': api.c:(.text+0x9d): undefined reference to `ompi_mpi_comm_null' api.c:(.text+0xbc): undefined reference to `ompi_mpi_comm_null' /home/dps/fftw3/lib/libfftw3_mpi.a(api.o):api.c:(.text+0xd3): more undefined references to `ompi_mpi_comm_null' follow /home/dps/fftw3/lib/libfftw3_mpi.a(api.o): In function `wisdom_ok_hook': api.c:(.text+0x1cc): undefined reference to `ompi_mpi_unsigned' api.c:(.text+0x21f): undefined reference to `ompi_mpi_op_land' api.c:(.text+0x226): undefined reference to `ompi_mpi_int' api.c:(.text+0x24b): undefined reference to `ompi_mpi_comm_null' /home/dps/fftw3/lib/libfftw3_mpi.a(api.o): In function `cost_hook': api.c:(.text+0x2c7): undefined reference to `ompi_mpi_comm_null' api.c:(.text+0x2dc): undefined reference to `ompi_mpi_comm_null' api.c:(.text+0x2ee): undefined reference to `ompi_mpi_op_max' api.c:(.text+0x2f5): undefined reference to `ompi_mpi_op_sum' api.c:(.text+0x308): undefined reference to `ompi_mpi_double' api.c:(.text+0x33b): undefined reference to `ompi_mpi_comm_null' /home/dps/fftw3/lib/libfftw3_mpi.a(f03-wrap.o): In function `fftw_mpi_local_size_many_transposed_f03': f03-wrap.c:(.text+0x3a): undefined reference to `MPI_Comm_f2c' /home/dps/fftw3/lib/libfftw3_mpi.a(f03-wrap.o): In function `fftw_mpi_local_size_many_f03': f03-wrap.c:(.text+0xa5): undefined reference to `MPI_Comm_f2c' /home/dps/fftw3/lib/libfftw3_mpi.a(f03-wrap.o): In function `fftw_mpi_local_size_transposed_f03': f03-wrap.c:(.text+0x103): undefined reference to `MPI_Comm_f2c' /home/dps/fftw3/lib/libfftw3_mpi.a(f03-wrap.o): In function `fftw_mpi_local_size_f03': f03-wrap.c:(.text+0x148): undefined reference to `MPI_Comm_f2c' /home/dps/fftw3/lib/libfftw3_mpi.a(f03-wrap.o): In function `fftw_mpi_local_size_many_1d_f03': f03-wrap.c:(.text+0x1a2): undefined reference to `MPI_Comm_f2c' /home/dps/fftw3/lib/libfftw3_mpi.a(f03-wrap.o):f03-wrap.c:(.text+0x20a): more undefined references to `MPI_Comm_f2c' follow /home/dps/fftw3/lib/libfftw3_mpi.a(transpose-alltoall.o): In function `apply': transpose-alltoall.c:(.text+0x83): undefined reference to `ompi_mpi_double' transpose-alltoall.c:(.text+0x11f): undefined reference to `ompi_mpi_double' transpose-alltoall.c:(.text+0x16d): undefined reference to `ompi_mpi_double' transpose-alltoall.c:(.text+0x19f): undefined reference to `ompi_mpi_double' /home/dps/fftw3/lib/libfftw3_mpi.a(transpose-pairwise.o): In function `transpose_chunks': transpose-pairwise.c:(.text+0x53a): undefined reference to `ompi_mpi_double' /home/dps/fftw3/lib/libfftw3_mpi.a(transpose-pairwise.o):transpose-pairwise.c:(.text+0x54c): more undefined references to `ompi_mpi_double' follow /home/dps/fftw3/lib/libfftw3_mpi.a(any-true.o): In function `fftw_mpi_any_true': any-true.c:(.text+0xa): undefined reference to `ompi_mpi_op_lor' any-true.c:(.text+0x1f): undefined reference to `ompi_mpi_int' /home/dps/fftw3/lib/libfftw3_mpi.a(wisdom-api.o): In function `fftw_mpi_gather_wisdom': wisdom-api.c:(.text+0x92): undefined reference to `ompi_mpi_unsigned_long' wisdom-api.c:(.text+0xcd): undefined reference to `ompi_mpi_char' wisdom-api.c:(.text+0x12d): undefined reference to `ompi_mpi_unsigned_long' wisdom-api.c:(.text+0x158): undefined reference to `ompi_mpi_char' /home/dps/fftw3/lib/libfftw3_mpi.a(wisdom-api.o): In function `fftw_mpi_broadcast_wisdom': wisdom-api.c:(.text+0x222): undefined reference to `ompi_mpi_unsigned_long' wisdom-api.c:(.text+0x24d): undefined reference to `ompi_mpi_char' wisdom-api.c:(.text+0x2b5): undefined reference to `ompi_mpi_unsigned_long' wisdom-api.c:(.text+0x2da): undefined reference to `ompi_mpi_char' Makefile:117: recipe for target 'nlvdw_mpi' failed make[1]: *** [nlvdw_mpi] Error 1 make[1]: Leaving directory '/home/dps/WIEN2K/SRC_nlvdw' Makefile:108: recipe for target 'para' failed make: *** [para] Error 2 On Wed, May 29, 2019 at 5:34 PM Gavin Abo wrote: > Look inside those compile.msg files as they likely contain messages > showing why they failed to compile. > On 5/28/2019 11:46 AM, Indranil mal wrote: > > Thank you for kind response > After following all the instructions given by you I have installed WIEN2k > with Intel parallel compiler. After compiling I got > > Compile time errors (if any) were: > SRC_lapw0/compile.msg:make[1]: *** [lapw0_mpi] Error 1 > SRC_lapw0/compile.msg:make: *** [para] Error 2 > SRC_nlvdw/compile.msg:make[1]: *** [nlvdw_mpi] Error 1 > > > ___ > 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
Re: [Wien] System configuration
Thank you for kind response After following all the instructions given by you I have installed WIEN2k with Intel parallel compiler. After compiling I got Compile time errors (if any) were: SRC_lapw0/compile.msg:make[1]: *** [lapw0_mpi] Error 1 SRC_lapw0/compile.msg:make: *** [para] Error 2 SRC_nlvdw/compile.msg:make[1]: *** [nlvdw_mpi] Error 1 On Tue, May 28, 2019 at 11:14 PM Indranil mal wrote: > Thank you for kind response > After following all the instructions given by you I have installed WIEN2k > with Intel parallel compiler. After compiling I got > > Compile time errors (if any) were: > SRC_lapw0/compile.msg:make[1]: *** [lapw0_mpi] Error 1 > SRC_lapw0/compile.msg:make: *** [para] Error 2 > SRC_nlvdw/compile.msg:make[1]: *** [nlvdw_mpi] Error 1 > SRC_nlvdw/compile.msg:make: *** [para] Error 2 > > > > On Tue, May 28, 2019 at 11:48 AM Gavin Abo wrote: > >> Continuing from post [1], I did a parallel mpi compile of WIEN2k 18.2 >> with fftw 3.3.8 (without ELPA), where -gcc-sys had to be added to CFLAGS >> [2], and siteconfig completed having no compile errors as seen below. >> >> username@computername:~$ cd ~ >> username@computername:~$ wget http://www.fftw.org/fftw-3.3.8.tar.gz >> ... >> username@computername:~$ tar xvf fftw-3.3.8.tar.gz >> ... >> username@computername:~$ mv fftw-3.3.8 fftw3 >> username@computername:~$ cd fftw3 >> username@computername:~/fftw3$ ./configure FCC=ifort CC=icc MPICC=mpiicc >> CFLAGS="-gcc-sys" --enable-mpi --prefix=$HOME/fftw3 >> ... >> username@computername:~/fftw3$ make >> ... >> username@computername:~/fftw3$ make install >> ... >> username@computername:~/fftw3$ ls -l ~/fftw3/include ~/fftw3/lib >> /home/username/fftw3/include: >> total 220 >> -rw-r--r-- 1 username username 2447 May 27 22:57 fftw3.f >> -rw-r--r-- 1 username username 54596 May 27 22:57 fftw3.f03 >> -rw-r--r-- 1 username username 31394 May 27 22:57 fftw3.h >> -rw-r--r-- 1 username username 26983 May 27 22:57 fftw3l.f03 >> -rw-r--r-- 1 username username 18678 May 27 22:57 fftw3l-mpi.f03 >> -rw-r--r-- 1 username username 36969 May 27 22:57 fftw3-mpi.f03 >> -rw-r--r-- 1 username username 9624 May 27 22:57 fftw3-mpi.h >> -rw-r--r-- 1 username username 25682 May 27 22:57 fftw3q.f03 >> >> /home/username/fftw3/lib: >> total 2108 >> drwxr-xr-x 3 username username4096 May 27 22:57 cmake >> -rw-r--r-- 1 username username 1933432 May 27 22:57 libfftw3.a >> -rwxr-xr-x 1 username username 893 May 27 22:57 libfftw3.la >> -rw-r--r-- 1 username username 201232 May 27 22:57 libfftw3_mpi.a >> -rwxr-xr-x 1 username username 939 May 27 22:57 libfftw3_mpi.la >> drwxr-xr-x 2 username username4096 May 27 22:57 pkgconfig >> username@computername:~/fftw3$ cd ~/WIEN2k >> username@computername:~/WIEN2k$ ./siteconfig >> ... >>Selection: P >> ... >>Shared Memory Architecture? (y/N):N >>Do you know/need a command to bind your jobs to specific nodes? >>(like taskset -c). Enter N / your_specific_command: N >> ... >>Set MPI_REMOTE to 0 / 1: 1 >> ... >> Remote shell (default is ssh) = ssh >> ... >> Remote copy (default is scp) = scp >> ... >> Do you have MPI, ScaLAPACK, ELPA, or FFTW installed and intend to run >> finegrained parallel? >> >> This is useful only for BIG cases (50 atoms and more / unit cell) >> and your HARDWARE has at least 16 cores (or is a cluster with >> Infiniband) >> You need to KNOW details about your installed MPI, ELPA, and FFTW ) >> >> (y/N) y >> ... >> Your compiler: mpiifort >> ... >> Do you want to use a present ScaLAPACK installation? (Y,n): Y >> ... >> Do you want to use the MKL version of ScaLAPACK? (Y,n):Y >> ... >> Do you use Intel MPI? (Y,n):Y >> ... >>Your SCALAPACK_LIBS are:-lmkl_scalapack_lp64 >> -lmkl_blacs_intelmpi_lp64 >> >>These options derive from your chosen settings: >> >>SCALAPACKROOT: >> /opt/intel/compilers_and_libraries_2019.4.243/linux/mkl/lib/ >>SCALAPACK_LIBNAME: mkl_scalapack_lp64 >>BLACSROOT: /opt/intel/compilers_and_libraries_2019.4.243/linux/mkl/lib/ >>BLACS_LIBNAME: mkl_blacs_intelmpi_lp64 >>MKL_TARGET_ARCH: intel64 >> Is this correct? (Y,n): Y >> Do you want to use a present FFTW installation? (Y,n): Y >> To abort the FFTW setup enter 'x' at any point! >> Do you want to automatically search for FFTW installations? (Y,n): >> Y >> Please specify a comma separated list of dire
Re: [Wien] System configuration
Sir, I am unable to compile libxc any 4.x ./configure FC= ifort CC=icc but they can be easily compiled with the help of autoconfiguration ./ configure with ifort and icc getting the following error configure: error: in `/home/dps/libxc-4.1.1': configure: error: C compiler cannot create executables See `config.log' for more details Also unable to install ELPA On Sat, May 25, 2019 at 6:08 PM Gavin Abo wrote: > As the error message says, the libxc library was compiled with a > different compiler. Perhaps you compiled it with gfortran (FC=gfortran). > Recompile it with ifort [ > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17716.html > ]. > > WIEN2k versions after 17 can use the 4.x version of libxc [ > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16924.html > ]. I haven't tried the latest released 4.3.4. If issues are encountered > compiling WIEN2k with it, fallback on an earlier 4.x version [ > https://tddft.org/programs/libxc/download/previous/ ]. > > It also says that it cannot find FFTW3 mpi. The fftw3 operating system > package (such as installed by apt or yum) usually only works for gfortran > and non-mpi. The FFTW can be downloaded [ > http://www.fftw.org/download.html ] and ifort compiled with --enable-mpi > [ > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16746.html > ]. > > > On 5/25/2019 2:55 AM, Indranil mal wrote: > > ... > I got the error > > SRC_lapw0/compile.msg:inputpars.F(6): error #7013: This module file was > not generated by any release of this compiler. [XC_F03_LIB_M] > SRC_lapw0/compile.msg:inputpars.F(17): error #6457: This derived type name > has not been declared. [XC_F03_FUNC_T] > ... > SRC_lapw0/compile.msg:/tmp/ifort1JKsyy.i(862): catastrophic error: Too > many errors, exiting > > SRC_lapw0/compile.msg:make[1]: *** [inputpars.o] Error 1 > SRC_lapw0/compile.msg:make: *** [para] Error 2 > SRC_lapw2/compile.msg:make[1]: *** [lapw2_mpi] Error 1 > SRC_lapw2/compile.msg:make: *** [rp] Error 2 > SRC_lapw2/compile.msg:make[1]: *** [lapw2c_mpi] Error 1 > SRC_lapw2/compile.msg:make: *** [cp] Error 2 > SRC_nlvdw/compile.msg:fft_modules.F(69): error #5102: Cannot open include > file 'fftw3-mpi.f03' > SRC_nlvdw/compile.msg:fft_modules.F(86): error #6404: This name does not > have a type, and must have an explicit type. [FFTW_MPI_LOCAL_SIZE_3D] > SRC_nlvdw/compile.msg:fft_modules.F(89): error #6404: This name does not > have a type, and must have an explicit type. [FFTW_ALLOC_COMPLEX] > SRC_nlvdw/compile.msg:fft_modules.F(120): error #6404: This name does not > have a type, and must have an explicit type. [FFTW_FORWARD] > SRC_nlvdw/compile.msg:fft_modules.F(121): error #6404: This name does not > have a type, and must have an explicit type. [FFTW_ESTIMATE] > SRC_nlvdw/compile.msg:fft_modules.F(117): error #6404: This name does not > have a type, and must have an explicit type. [FFTW_MPI_PLAN_DFT_3D] > SRC_nlvdw/compile.msg:fft_modules.F(125): error #6404: This name does not > have a type, and must have an explicit type. [FFTW_BACKWARD] > SRC_nlvdw/compile.msg:fft_modules.F(133): error #6601: In a CASE > statement, the case-value must be a constant expression. [FFTW_FORWARD] > SRC_nlvdw/compile.msg:fft_modules.F(133): error #6612: In a CASE > statement, the case-value must be of type INTEGER, CHARACTER, or LOGICAL. > [FFTW_FORWARD] > SRC_nlvdw/compile.msg:fft_modules.F(133): error #6611: The case-value must > be of the same type as the case-expr. [FFTW_FORWARD] > SRC_nlvdw/compile.msg:fft_modules.F(135): error #6601: In a CASE > statement, the case-value must be a constant expression. [FFTW_BACKWARD] > SRC_nlvdw/compile.msg:fft_modules.F(135): error #6612: In a CASE > statement, the case-value must be of type INTEGER, CHARACTER, or LOGICAL. > [FFTW_BACKWARD] > SRC_nlvdw/compile.msg:fft_modules.F(135): error #6611: The case-value must > be of the same type as the case-expr. [FFTW_BACKWARD] > SRC_nlvdw/compile.msg:make[1]: *** [fft_modules.o] Error 1 > SRC_nlvdw/compile.msg:make: *** [para] Error 2 > SRC_nmr/compile.msg:make[1]: *** [nmr_mpi] Error 1 > SRC_nmr/compile.msg:make: *** [rp] Error 2 > SRC_nmr/compile.msg:make[1]: *** [nmrc_mpi] Error 1 > SRC_nmr/compile.msg:make: *** [cp] Error 2 > > please 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 > ___ 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
the corresponding compiler and linker options are as follows Recommended options for system linuxifc are: Compiler options:-O1 -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -assume buffered_io -I$(MKLROOT)/include Linker Flags:$(FOPT) -L$(MKLROOT)/lib/$(MKL_TARGET_ARCH) -lpthread -lm -ldl -liomp5 Preprocessor flags: '-DParallel' R_LIB (LAPACK+BLAS): -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core Current settings: O Compiler options:-O1 -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -assume buffered_io -I$(MKLROOT)/include L Linker Flags:$(FOPT) -L$(MKLROOT)/lib/$(MKL_TARGET_ARCH) -lpthread -lm -ldl -liomp5 P Preprocessor flags '-DParallel' R R_LIBS (LAPACK+BLAS):-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core X LIBX options:-DLIBXC -I/opt/etsf/include LIBXC-LIBS: -L/opt/etsf/lib/ -lxcf03 -lxc On Sat, May 25, 2019 at 2:25 PM Indranil mal wrote: > After setting the compiler ifort and icc and setting the parallel config > as follows > Current settings: > > Parallel compiler : mpiifort > SCALAPACK_LIBS : -lmkl_scalapack_lp64 > -lmkl_blacs_intelmpi_lp64 > FFTW_OPT : -DFFTW3 -I/opt/fftw/include > FFTW_LIBS : -L/opt/fftw/lib64 -lfftw3 > FFTW_PLIBS : -lfftw3_mpi > ELPA_OPT : > ELPA_LIBS : > FPOPT(par.comp.options): -O1 -FR -mp1 -w -prec_div -pc80 -pad -ip > -DINTEL_VML -traceback -assume buffered_io -I$(MKLROOT)/include > MPIRUN command : mpirun -np _NP_ -machinefile _HOSTS_ > _EXEC_ > > without installing ELPA and linked fftw3 of intel parallel studio > I got the error > > SRC_lapw0/compile.msg:inputpars.F(6): error #7013: This module file was > not generated by any release of this compiler. [XC_F03_LIB_M] > SRC_lapw0/compile.msg:inputpars.F(17): error #6457: This derived type name > has not been declared. [XC_F03_FUNC_T] > SRC_lapw0/compile.msg:inputpars.F(18): error #6457: This derived type name > has not been declared. [XC_F03_FUNC_INFO_T] > SRC_lapw0/compile.msg:inputpars.F(162): error #6404: This name does not > have a type, and must have an explicit type. [XC_FUNC] > SRC_lapw0/compile.msg:inputpars.F(162): error #6404: This name does not > have a type, and must have an explicit type. [XC_UNPOLARIZED] > SRC_lapw0/compile.msg:inputpars.F(163): error #6404: This name does not > have a type, and must have an explicit type. [XC_INFO] > SRC_lapw0/compile.msg:inputpars.F(163): error #6404: This name does not > have a type, and must have an explicit type. [XC_F03_FUNC_GET_INFO] > SRC_lapw0/compile.msg:inputpars.F(164): error #6404: This name does not > have a type, and must have an explicit type. [XC_F03_FUNC_INFO_GET_FAMILY] > SRC_lapw0/compile.msg:inputpars.F(164): error #6608: In a CASE statement, > the case-expr must be of type INTEGER, CHARACTER, or LOGICAL. > [XC_F03_FUNC_INFO_GET_FAMILY] > SRC_lapw0/compile.msg:inputpars.F(165): error #6404: This name does not > have a type, and must have an explicit type. [XC_FAMILY_MGGA] > SRC_lapw0/compile.msg:inputpars.F(165): error #6601: In a CASE statement, > the case-value must be a constant expression. [XC_FAMILY_MGGA] > SRC_lapw0/compile.msg:inputpars.F(165): error #6612: In a CASE statement, > the case-value must be of type INTEGER, CHARACTER, or LOGICAL. > [XC_FAMILY_MGGA] > SRC_lapw0/compile.msg:inputpars.F(165): error #6404: This name does not > have a type, and must have an explicit type. [XC_FAMILY_HYB_MGGA] > SRC_lapw0/compile.msg:inputpars.F(165): error #6601: In a CASE statement, > the case-value must be a constant expression. [XC_FAMILY_HYB_MGGA] > SRC_lapw0/compile.msg:inputpars.F(165): error #6612: In a CASE statement, > the case-value must be of type INTEGER, CHARACTER, or LOGICAL. > [XC_FAMILY_HYB_MGGA] > SRC_lapw0/compile.msg:inputpars.F(174): error #6608: In a CASE statement, > the case-expr must be of type INTEGER, CHARACTER, or LOGICAL. > [XC_F03_FUNC_INFO_GET_FAMILY] > SRC_lapw0/compile.msg:inputpars.F(175): error #6601: In a CASE statement, > the case-value must be a constant expression. [XC_FAMILY_MGGA] > SRC_lapw0/compile.msg:inputpars.F(175): error #6612: In a CASE statement, > the case-value must be of type INTEGER, CHARACTER, or LOGICAL. > [XC_FAMILY_MGGA] > SRC_lapw0/compile.msg:inputpars.F(175): error #6601: In a CASE statement, > the case-value must be a constant expression. [XC_FAMILY_HYB_MGGA] > SRC_lapw0/compile.msg:inputpars.F(175): error #6612: In a CASE statement, > the case-value must be of type INTEGER, CHARACTER, or LOGICAL. > [XC_FAMILY_HYB_MGGA] > SRC_lapw0/compile.msg:
Re: [Wien] System configuration
pi programs. It is likely that the serial stuff still built fine. > > BTW Even after fixing the flags (using for example instruction in the > > Gavins email) you will still miss the mpi libraries, therefore it will > > not help much. Unfortunately, I don't know how to disable the parallel > > build after it has been enabled (and in general the siteconfig is not > > very good at clearing completely already set options), so you just have > > to ignore the errors for now and hope that the rest is fine (or clean > > your Wien2k folder, start from scratch with fresh gfortran config, and > > when it asks you about finegrained parallel just say no). > > > > The more important thing is, after using the new compile flags I have > > suggested in an earlier email, together with -lopenblas instead of the > > -lapack -lblas flags for the linker (and optionally with the provided > > patch), is the lapw1 faster? > > > > Best regards > > Pavel > > > > On Thu, 2019-05-23 at 20:18 -0600, Gavin Abo wrote: > >> The -mp1, -pad, -traceback, and so on look like ifort specific > >> compiler flags . > >> If you are using gfortran, compiler flags for gfortran need to be > >> used for the Compiling Options in siteconfig. A good starting > >> pointing is to use the "Recommended options" by siteconfig for > >> linuxgfortran, which is seen in the post [1], before you start > >> customizing it with your own flags. For example, gfortan has > >> -fbacktrace [2] instead of the -trackback that ifort has [3]. > >> [1] > >> > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17903.html > >> [2] https://gcc.gnu.org/onlinedocs/gfortran/Option-Summary.html > >> [3] > >> > https://software.intel.com/en-us/fortran-compiler-developer-guide-and-reference-traceback > >> > >> On 5/23/2019 12:37 PM, Indranil mal wrote: > >>> I did the patching but after compiling I am getting the > >>> SRC_dstart/compile.msg:gfortran: error: buffered_io: No such file > >>> or directory > >>> SRC_dstart/compile.msg:gfortran: error: unrecognized command line > >>> option ‘-mp1’ > >>> SRC_dstart/compile.msg:gfortran: error: unrecognized command line > >>> option ‘-prec_div’; did you mean ‘-mrecip’? > >>> SRC_dstart/compile.msg:gfortran: error: unrecognized command line > >>> option ‘-pc80’; did you mean ‘-mpc80’? > >>> SRC_dstart/compile.msg:gfortran: error: unrecognized command line > >>> option ‘-pad’ > >>> SRC_dstart/compile.msg:gfortran: error: unrecognized command line > >>> option ‘-ip’; did you mean ‘-p’? > >>> SRC_dstart/compile.msg:gfortran: error: unrecognized command line > >>> option ‘-traceback’ > >>> SRC_dstart/compile.msg:gfortran: error: unrecognized command line > >>> option ‘-assume’; did you mean ‘-msse’? > >>> SRC_dstart/compile.msg:make[1]: *** [module.o] Error 1 > >>> SRC_dstart/compile.msg:make: *** [para] Error 2 > >>> ... > ___ > 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] System configuration
t; > And after each run show total timings as well as > $ grep "TIME HAMILT" test_case.output1 > Hopefully, you are already linking the multithreaded Openblas (but > dunno what is the Ubuntu default)... > > I'll help you with the parallel execution in the next step. > > Best regards > Pavel > > On Thu, 2019-05-23 at 18:58 +0530, Indranil mal wrote: > > Dear sir > > > > After running x lapw1 I got the following > > > > ~/test_case$ x lapw1 > > STOP LAPW1 END > > 114.577u 0.247s 1:54.82 99.9% 0+0k 0+51864io 0pf+0w > > > > I am using parallel k point execution only 8 GB memory is in use and > > for 100 atom (100 kpoints) calculation it is taking around 12 hours > > to complete one cycle. > > please help me. > > > > Thanking you > > > > Indranil > > > > On Thu, May 23, 2019 at 11:22 AM Pavel Ondračka < > > pavel.ondra...@email.cz> wrote: > > > Hi Indranil, > > > > > > While the k-point parallelization is usually the most efficient > > > (provided you have sufficient number of k-points) and does not need > > > any > > > extra libraries, for 100atoms case it might be problematic to fit > > > 12 > > > processes into 32GB of memory. I assume you are already using it > > > since > > > you claim to run on two cores? > > > > > > Instead check what is the maximum memory requirement of lapw1 when > > > run > > > in serial and based on that find how much processes you can run in > > > parallel, than for each place one line "1:localhost" into .machines > > > file (there is no need to copy .machines from templates, or use > > > random > > > scripts, instead read the userguide to understand what you are > > > doing, > > > it will save you time in the long run). If you can run at least few > > > k- > > > points in parallel it might be enough to speed it up significantly. > > > > > > For MPI you would need openmpi-devel scalapack-devel and fftw3- > > > devel > > > (I'm not sure how exactly are they named on Ubuntu) packages. > > > Especially the scalapack configuration could be tricky, it is > > > probably > > > easiest to start with lapw0 as this needs only MPI and fftw. > > > > > > Also based on my experience with default gfortran settings, it is > > > likely that you don't have even optimized the single core > > > performance, > > > try to download the serial benchmark > > > http://susi.theochem.tuwien.ac.at/reg_user/benchmark/test_case.tar.gz > > > untar, run x lapw1 and report timings (on average i7 CPU it should > > > take > > > below 30 seconds, if it takes significantly more, you will need > > > some > > > more tweaks). > > > > > > Best regards > > > Pavel > > > > > > On Thu, 2019-05-23 at 10:42 +0530, Dr. K. C. Bhamu wrote: > > > > Hii, > > > > > > > > If you are doing k-point parallel calculation (having number of > > > k- > > > > points in IBZ more then 12) then use below script on terminal > > > where > > > > you want to run the calculation or use in your job script with > > > -p > > > > option in run(sp)_lapw (-so). > > > > > > > > if anyone knows how to repeat a nth line m times in a file then > > > this > > > > script can be changed. > > > > > > > > Below script simply coping machine file from temple directory and > > > > updating it as per your need. > > > > So you do not need copy it, open it in your favorite editor and > > > do it > > > > manually. > > > > > > > > cp $WIENROOT/SRC_templates/.machines . ; grep localhost .machines > > > | > > > > perl -ne 'print $_ x 6' > LOCALHOST.dat ; tail -n 2 .machines > > > > > grang.dat ; sed '22,25d' .machines > MACHINE.dat ; cat > > > MACHINE.dat > > > > localhost.dat grang.dat > .machines ; rm LOCALHOST.dat > > > MACHINE.dat > > > > grang.dat > > > > > > > > regards > > > > Bhamu > > > > > > > > > > > > On Wed, May 22, 2019 at 10:52 PM Indranil mal < > > > indranil@gmail.com > > > > > wrote: > > > > > respected sir/ Users, > > > > > I am using a PC with intel i7 8th gen (with > > > 12 > > > > > cores) 32GB RAM and 2TB HDD with UBU
[Wien] System configuration
respected sir/ Users, I am using a PC with intel i7 8th gen (with 12 cores) 32GB RAM and 2TB HDD with UBUNTU 18.04 LTS. I have installed OpenBLAS-0.2.20 and using GNU FORTRAN and c compiler. I am trying to run a system with 100 atoms only two cores are using the rest of them are idle and the calculation taking a too long time. I have not installed mpi ScaLAPACK or elpa. Please help me what should I do to utilize all of the cores of my cpu. 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] Regarding Super cell
36000 LT. NN-DIST= 4.61573 RMT( 4)=2.18000 AND RMT( 23)=2.18000 ATOM 4 Ga3ATOM 23 As6 SUMS TO 4.36000 LT. NN-DIST= 4.61573 RMT( 3)=2.18000 AND RMT( 22)=2.18000 ATOM 3 Ga2ATOM 22 As5 SUMS TO 3.68000 LT. NN-DIST= 4.61573 RMT( 2)=1.5 AND RMT( 19)=2.18000 ATOM 2 B 1ATOM 19 As2 SUMS TO 4.36000 LT. NN-DIST= 4.61573 RMT( 1)=2.18000 AND RMT( 18)=2.18000 ATOM 1 Ga1ATOM 18 As1 NAMED ATOM: As12 Z changed to IATNR+999 to determine equivalency NAMED ATOM: As11 Z changed to IATNR+999 to determine equivalency NAMED ATOM: As10 Z changed to IATNR+999 to determine equivalency NAMED ATOM: As9 Z changed to IATNR+999 to determine equivalency NAMED ATOM: As8 Z changed to IATNR+999 to determine equivalency NAMED ATOM: As7 Z changed to IATNR+999 to determine equivalency NAMED ATOM: As6 Z changed to IATNR+999 to determine equivalency NAMED ATOM: As5 Z changed to IATNR+999 to determine equivalency NAMED ATOM: As4 Z changed to IATNR+999 to determine equivalency NAMED ATOM: As3 Z changed to IATNR+999 to determine equivalency NAMED ATOM: As2 Z changed to IATNR+999 to determine equivalency NAMED ATOM: As1 Z changed to IATNR+999 to determine equivalency NAMED ATOM: Ga16 Z changed to IATNR+999 to determine equivalency NAMED ATOM: Ga15 Z changed to IATNR+999 to determine equivalency NAMED ATOM: Ga14 Z changed to IATNR+999 to determine equivalency NAMED ATOM: Ga13 Z changed to IATNR+999 to determine equivalency NAMED ATOM: Ga12 Z changed to IATNR+999 to determine equivalency NAMED ATOM: Ga11 Z changed to IATNR+999 to determine equivalency NAMED ATOM: Ga10 Z changed to IATNR+999 to determine equivalency NAMED ATOM: Ga9 Z changed to IATNR+999 to determine equivalency NAMED ATOM: Ga8 Z changed to IATNR+999 to determine equivalency NAMED ATOM: Ga7 Z changed to IATNR+999 to determine equivalency NAMED ATOM: Ga6 Z changed to IATNR+999 to determine equivalency NAMED ATOM: Ga5 Z changed to IATNR+999 to determine equivalency NAMED ATOM: Ga4 Z changed to IATNR+999 to determine equivalency NAMED ATOM: Ga3 Z changed to IATNR+999 to determine equivalency NAMED ATOM: Ga2 Z changed to IATNR+999 to determine equivalency NAMED ATOM: B 1 Z changed to IATNR+999 to determine equivalency NAMED ATOM: Ga1 Z changed to IATNR+999 to determine equivalency iix,iiy,iiz 2 2 3 63.9574258 63.957425863.9574258 DSTMAX: 35.49637143003 specify nn-bondlength factor: (usually=2) [and optionally dlimit, dstmax (about 1.d-5, 20)] next is nn next is setrmt On Mon, May 20, 2019 at 1:01 AM wrote: > If I execute init_lapw using Super_Cell_Replaced_By_One_Atom.struct > then there is no problem. Copy the struct file in a new directory > and do init_lapw. > > > On Sunday 2019-05-19 19:11, Indranil mal wrote: > > >Date: Sun, 19 May 2019 19:11:34 > >From: Indranil mal > >To: t...@theochem.tuwien.ac.at > >Subject: Re: [Wien] Regarding Super cell > > > > > > > >On Sun, May 19, 2019 at 10:39 PM Indranil mal > wrote: > > > > > >On Sun, May 19, 2019 at 8:33 PM wrote: > > Hi, > > > > The message > > "At line 130 of file insld.f (unit = 20, file = > 'B1Ga72As_LDA_MBJ.struct')" > > says that there is something wrong in the struct file. Send it such > that > > we can have a look at it. > > > > F. Tran > > > > On Sunday 2019-05-19 15:32, Indranil mal wrote: > > > > >Date: Sun, 19 May 2019 15:32:08 > > >From: Indranil mal > > >Reply-To: A Mailing list for WIEN2k users < > wien@zeus.theochem.tuwien.ac.at> > > >To: A Mailing list for WIEN2k users < > wien@zeus.theochem.tuwien.ac.at> > > >Subject: [Wien] Regarding Super cell > > > > > >Dear sir/ Users > > > After making a 223 super cell for a (216 > F43m) space group I'm trying to replace one host atom (anion > > >or cation) with a smaller size atom then in Xcrysden the smaller > atom not showing bond to any atoms. Along with this the > > >structure file changes by xnn if I do accept the and start > xsgroup then the space group changes after accepting that I am > > >getting the error > > >Commandline: x lstart -p > > >Program input is: "5 -6.0 " > > > > > > SELECT XCPOT: > > > recommended: PBE[(13) GGA of Perdew-Burke-Ernzerhof 96] > > > LDA[( 5)] > > >
[Wien] Regarding Super cell
Dear sir/ Users After making a 223 super cell for a (216 F43m) space group I'm trying to replace one host atom (anion or cation) with a smaller size atom then in Xcrysden the smaller atom not showing bond to any atoms. Along with this the structure file changes by xnn if I do accept the and start xsgroup then the space group changes after accepting that I am getting the error Commandline: x lstart -p Program input is: "5 -6.0 " SELECT XCPOT: recommended: PBE[(13) GGA of Perdew-Burke-Ernzerhof 96] LDA[( 5)] WC [(11) GGA of Wu-Cohen 2006] PBESOL [(19) GGA of Perdew etal. 2008] SELECT ENERGY to separate core and valence states: recommended: -6.0 Ry (check how much core charge leaks out of MT-sphere) ALTERNATIVELY: specify charge localization (between 0.97 and 1.0) to select core state At line 130 of file insld.f (unit = 20, file = 'B1Ga72As_LDA_MBJ.struct') Fortran runtime error: End of file Error termination. Backtrace: #0 0x14f62065831a #1 0x14f620658ec5 #2 0x14f62065968d #3 0x14f6207cfa33 #4 0x14f6207d001a #5 0x14f6207ccfcd #6 0x14f6207d112c #7 0x14f6207d24bc #8 0x562615f286ca #9 0x562615f2ed95 #10 0x562615f23e2e #11 0x14f61fcb7b96 #12 0x562615f23e59 #13 0x 0.064u 0.000s 0:00.06 100.0% 0+0k 0+512io 0pf+0w error: command /home/dps/WIEN2K/lstart lstart.def failed How ever If I do not accept the space group change then I got the error MULT not equal please check xnn out file. please 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
Re: [Wien] Fwd: Installation issue
Thank you sir. The problem was with XCRYSDEN_TOPDIR. Now solved. Thanking you Indranil On Tue, Apr 30, 2019 at 12:33 PM Gavin Abo wrote: > In your .bashrc, check if you have: > > XCRYSDEN_TOPDIR=/usr/share/xcrysden > XCRYSDEN_LIB_BINDIR=/usr/lib/xcrysden > export XCRYSDEN_TOPDIR XCRYSDEN_LIB_BINDIR > > If not, you might try that. Make sure you kill and restart w2web after > making the change to .bashrc. > > If that doesn't work, it may be easier to uninstall xcrysden with your > package manager (e.g. sudo apt remove xcrysden) and install the xcrysden > semishared binary package [ > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17895.html > ]. > > However, you have to compile from source (xcrysden-1.5.60.tar.gz) [ > http://www.xcrysden.org/Download.html , > http://www.xcrysden.org/doc/install.html#__toc__6 ] if you want to patch > it: > > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18004.html > On 4/29/2019 11:11 PM, Indranil mal wrote: > > yes sir. still the problem is there. No issue sir I can manually see the > structures. > > > Thanking you > Indranil > > On Mon, Apr 29, 2019 at 8:37 PM Peter Blaha > wrote: > >> Did you do the killing and restart of w2web ??? >> >> Am 29.04.2019 um 14:24 schrieb Indranil mal: >> > By using the command line "xcrysden --wien_struct case.struct" I can >> see >> > the structures and the view structure button is also showing in w2web. >> > But When click on the view structure button "Requires X-Windows system >> > ... " message is coming. >> > >> > Thanking you >> > >> > Indranil >> > >> > On Fri, Apr 26, 2019 at 11:02 AM Peter Blaha >> > mailto:pbl...@theochem.tuwien.ac.at>> >> wrote: >> > >> > change into a directory where you have a case.struct file. >> > Can you open it using: >> > >> > xcrysden --wien_struct case.struct >> > >> > If yes, then xcrysden is properly installed. If you do not see the >> > view >> > structure button in w2web, you have to kill w2web and restart it >> again: >> > >> > ps -ef|grep w2web # this gives you the "PID" of w2web, a number >> on >> > the left side >> > kill PID# >> > >> > and repeat the ps command until you do not find w2web anymore. Then >> > start w2web again by typing: >> > >> > w2web >> > >> > Regards >> > >> > Am 26.04.2019 um 06:00 schrieb Indranil mal: >> > > I have followed your suggestion and it is working except the >> > xcrysden is >> > > not linked, can not view structures. >> > > >> > > dps@dps-lab:~$ whereis xcrysden >> > > xcrysden: /usr/bin/xcrysden /usr/lib/xcrysden /usr/share/xcrysden >> > > /home/dps/WIEN2K/xcrysden /usr/share/man/man1/xcrysden.1.gz >> > > >> > > XCRYSDEN_TOPDIR=/usr/share/xcrysden >> > > XCRYSDEN_SCRATCH=/home/dps/xcrys_tmp >> > > >> > > unable to edit the top directory. However I have installed >> > xcrysden from >> > > UBUNTU software library. >> > > >> > > >> > > Thanking you >> > > >> > > Indranil >> > > >> > > >> > > On Tue, Apr 23, 2019 at 6:41 PM Peter Blaha >> > > > > <mailto:pbl...@theochem.tuwien.ac.at> >> > <mailto:pbl...@theochem.tuwien.ac.at >> > <mailto:pbl...@theochem.tuwien.ac.at>>> wrote: >> > > >> > > I suggest that you first do only the sequential installation. >> > > >> > > For this (and for your hardware) you don't need mpi, >> > scalapack or elpa. >> > > >> > > Change into SRC_lapw0 and inspect the compile.msg file in >> > more detail. >> > > You may see more informative messages then what you posted. >> > > >> > > You can also recompile again simply by typing "make" in >> > SRC_lapw0. >> > > >> > > PS: If this was the only error in siteconfig after >> > compilation of all >> > > programs, it might be your libxc installation. (remove >> > -DLIBXC, and the >
Re: [Wien] Fwd: Installation issue
yes sir. still the problem is there. No issue sir I can manually see the structures. Thanking you Indranil On Mon, Apr 29, 2019 at 8:37 PM Peter Blaha wrote: > Did you do the killing and restart of w2web ??? > > Am 29.04.2019 um 14:24 schrieb Indranil mal: > > By using the command line "xcrysden --wien_struct case.struct" I can see > > the structures and the view structure button is also showing in w2web. > > But When click on the view structure button "Requires X-Windows system > > ... " message is coming. > > > > Thanking you > > > > Indranil > > > > On Fri, Apr 26, 2019 at 11:02 AM Peter Blaha > > mailto:pbl...@theochem.tuwien.ac.at>> > wrote: > > > > change into a directory where you have a case.struct file. > > Can you open it using: > > > > xcrysden --wien_struct case.struct > > > > If yes, then xcrysden is properly installed. If you do not see the > > view > > structure button in w2web, you have to kill w2web and restart it > again: > > > > ps -ef|grep w2web # this gives you the "PID" of w2web, a number on > > the left side > > kill PID# > > > > and repeat the ps command until you do not find w2web anymore. Then > > start w2web again by typing: > > > > w2web > > > > Regards > > > > Am 26.04.2019 um 06:00 schrieb Indranil mal: > > > I have followed your suggestion and it is working except the > > xcrysden is > > > not linked, can not view structures. > > > > > > dps@dps-lab:~$ whereis xcrysden > > > xcrysden: /usr/bin/xcrysden /usr/lib/xcrysden /usr/share/xcrysden > > > /home/dps/WIEN2K/xcrysden /usr/share/man/man1/xcrysden.1.gz > > > > > > XCRYSDEN_TOPDIR=/usr/share/xcrysden > > > XCRYSDEN_SCRATCH=/home/dps/xcrys_tmp > > > > > > unable to edit the top directory. However I have installed > > xcrysden from > > > UBUNTU software library. > > > > > > > > > Thanking you > > > > > > Indranil > > > > > > > > > On Tue, Apr 23, 2019 at 6:41 PM Peter Blaha > > > > <mailto:pbl...@theochem.tuwien.ac.at> > > <mailto:pbl...@theochem.tuwien.ac.at > > <mailto:pbl...@theochem.tuwien.ac.at>>> wrote: > > > > > > I suggest that you first do only the sequential installation. > > > > > > For this (and for your hardware) you don't need mpi, > > scalapack or elpa. > > > > > > Change into SRC_lapw0 and inspect the compile.msg file in > > more detail. > > > You may see more informative messages then what you posted. > > > > > > You can also recompile again simply by typing "make" in > > SRC_lapw0. > > > > > > PS: If this was the only error in siteconfig after > > compilation of all > > > programs, it might be your libxc installation. (remove > > -DLIBXC, and the > > > corresponding includes and libraries in the Makefile of > > SRC_lapw0. > > > > > > On 4/23/19 10:00 AM, Indranil mal wrote: > > > > I am using a PC with intel i7 32GB RAM and 2TB HDD with > > UBUNTU 18.04 > > > > LTS. I have installed OpenBLAS-0.2.20 and using GNU > > FORTRAN and c > > > > compiler and my settings for compiler/Linker , Libraries > > are as > > > followed > > > > > > > > Current settings: > > > >O Compiler options:-ffree-form -O2 > > > -ffree-line-length-none > > > >L Linker Flags:$(FOPT) > > > >P Preprocessor flags '-DParallel' > > > >R R_LIBS (LAPACK+BLAS):-llapack -lblas -lpthread > > > >X LIBX options:-DLIBXC -I/opt/etsf/include > > > >LIBXC-LIBS: -L/opt/etsf/lib/ -lxcf03 > -lxc > > > > > > > > I have installed FFTW3 and mpi but could not install ELPA > > getting > > > the > > > > error " No usable BLACS
Re: [Wien] Fwd: Installation issue
By using the command line "xcrysden --wien_struct case.struct" I can see the structures and the view structure button is also showing in w2web. But When click on the view structure button "Requires X-Windows system ... " message is coming. Thanking you Indranil On Fri, Apr 26, 2019 at 11:02 AM Peter Blaha wrote: > change into a directory where you have a case.struct file. > Can you open it using: > > xcrysden --wien_struct case.struct > > If yes, then xcrysden is properly installed. If you do not see the view > structure button in w2web, you have to kill w2web and restart it again: > > ps -ef|grep w2web # this gives you the "PID" of w2web, a number on > the left side > kill PID# > > and repeat the ps command until you do not find w2web anymore. Then > start w2web again by typing: > > w2web > > Regards > > Am 26.04.2019 um 06:00 schrieb Indranil mal: > > I have followed your suggestion and it is working except the xcrysden is > > not linked, can not view structures. > > > > dps@dps-lab:~$ whereis xcrysden > > xcrysden: /usr/bin/xcrysden /usr/lib/xcrysden /usr/share/xcrysden > > /home/dps/WIEN2K/xcrysden /usr/share/man/man1/xcrysden.1.gz > > > > XCRYSDEN_TOPDIR=/usr/share/xcrysden > > XCRYSDEN_SCRATCH=/home/dps/xcrys_tmp > > > > unable to edit the top directory. However I have installed xcrysden from > > UBUNTU software library. > > > > > > Thanking you > > > > Indranil > > > > > > On Tue, Apr 23, 2019 at 6:41 PM Peter Blaha > > mailto:pbl...@theochem.tuwien.ac.at>> > wrote: > > > > I suggest that you first do only the sequential installation. > > > > For this (and for your hardware) you don't need mpi, scalapack or > elpa. > > > > Change into SRC_lapw0 and inspect the compile.msg file in more > detail. > > You may see more informative messages then what you posted. > > > > You can also recompile again simply by typing "make" in SRC_lapw0. > > > > PS: If this was the only error in siteconfig after compilation of all > > programs, it might be your libxc installation. (remove -DLIBXC, and > the > > corresponding includes and libraries in the Makefile of SRC_lapw0. > > > > On 4/23/19 10:00 AM, Indranil mal wrote: > > > I am using a PC with intel i7 32GB RAM and 2TB HDD with UBUNTU > 18.04 > > > LTS. I have installed OpenBLAS-0.2.20 and using GNU FORTRAN and c > > > compiler and my settings for compiler/Linker , Libraries are as > > followed > > > > > > Current settings: > > >O Compiler options:-ffree-form -O2 > > -ffree-line-length-none > > >L Linker Flags:$(FOPT) > > >P Preprocessor flags '-DParallel' > > >R R_LIBS (LAPACK+BLAS):-llapack -lblas -lpthread > > >X LIBX options:-DLIBXC -I/opt/etsf/include > > >LIBXC-LIBS: -L/opt/etsf/lib/ -lxcf03 -lxc > > > > > > I have installed FFTW3 and mpi but could not install ELPA getting > > the > > > error " No usable BLACS found. If installed in a non-standard > place, > > > please specify suitable LDFLAGS and FCFLAGS as arguments to > > configure". > > > And that is why I did not configure the parallel computing. > > > > > > When I am trying to compile the getting the following error and > > attached > > > the compile.msg file. Please help me to install WIEN2K in my > system. > > > > > > done. > > > > > > Compile time errors (if any) were: > > > SRC_lapw0/compile.msg:collect2: error: ld returned 1 exit status > > > SRC_lapw0/compile.msg:make[1]: *** [lapw0] Error 1 > > > SRC_lapw0/compile.msg:make: *** [seq] Error 2 > > > > > > Thanking you > > > > > > Indranil > > > > > > > > > ___ > > > Wien mailing list > > > Wien@zeus.theochem.tuwien.ac.at > > <mailto:Wien@zeus.theochem.tuwien.ac.at> > > > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > > > SEARCH the MAILING-LIST at: > > > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > > > > > > > -- > > > >
Re: [Wien] Fwd: Installation issue
I have followed your suggestion and it is working except the xcrysden is not linked, can not view structures. dps@dps-lab:~$ whereis xcrysden xcrysden: /usr/bin/xcrysden /usr/lib/xcrysden /usr/share/xcrysden /home/dps/WIEN2K/xcrysden /usr/share/man/man1/xcrysden.1.gz XCRYSDEN_TOPDIR=/usr/share/xcrysden XCRYSDEN_SCRATCH=/home/dps/xcrys_tmp unable to edit the top directory. However I have installed xcrysden from UBUNTU software library. Thanking you Indranil On Tue, Apr 23, 2019 at 6:41 PM Peter Blaha wrote: > I suggest that you first do only the sequential installation. > > For this (and for your hardware) you don't need mpi, scalapack or elpa. > > Change into SRC_lapw0 and inspect the compile.msg file in more detail. > You may see more informative messages then what you posted. > > You can also recompile again simply by typing "make" in SRC_lapw0. > > PS: If this was the only error in siteconfig after compilation of all > programs, it might be your libxc installation. (remove -DLIBXC, and the > corresponding includes and libraries in the Makefile of SRC_lapw0. > > On 4/23/19 10:00 AM, Indranil mal wrote: > > I am using a PC with intel i7 32GB RAM and 2TB HDD with UBUNTU 18.04 > > LTS. I have installed OpenBLAS-0.2.20 and using GNU FORTRAN and c > > compiler and my settings for compiler/Linker , Libraries are as followed > > > > Current settings: > >O Compiler options:-ffree-form -O2 -ffree-line-length-none > >L Linker Flags:$(FOPT) > >P Preprocessor flags '-DParallel' > >R R_LIBS (LAPACK+BLAS):-llapack -lblas -lpthread > >X LIBX options:-DLIBXC -I/opt/etsf/include > >LIBXC-LIBS: -L/opt/etsf/lib/ -lxcf03 -lxc > > > > I have installed FFTW3 and mpi but could not install ELPA getting the > > error " No usable BLACS found. If installed in a non-standard place, > > please specify suitable LDFLAGS and FCFLAGS as arguments to configure". > > And that is why I did not configure the parallel computing. > > > > When I am trying to compile the getting the following error and attached > > the compile.msg file. Please help me to install WIEN2K in my system. > > > > done. > > > > Compile time errors (if any) were: > > SRC_lapw0/compile.msg:collect2: error: ld returned 1 exit status > > SRC_lapw0/compile.msg:make[1]: *** [lapw0] Error 1 > > SRC_lapw0/compile.msg:make: *** [seq] Error 2 > > > > 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 > > > > -- > >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 > ___ 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] Fwd: Installation issue
I am using a PC with intel i7 32GB RAM and 2TB HDD with UBUNTU 18.04 LTS. I have installed OpenBLAS-0.2.20 and using GNU FORTRAN and c compiler and my settings for compiler/Linker , Libraries are as followed Current settings: O Compiler options:-ffree-form -O2 -ffree-line-length-none L Linker Flags:$(FOPT) P Preprocessor flags '-DParallel' R R_LIBS (LAPACK+BLAS):-llapack -lblas -lpthread X LIBX options:-DLIBXC -I/opt/etsf/include LIBXC-LIBS: -L/opt/etsf/lib/ -lxcf03 -lxc I have installed FFTW3 and mpi but could not install ELPA getting the error " No usable BLACS found. If installed in a non-standard place, please specify suitable LDFLAGS and FCFLAGS as arguments to configure". And that is why I did not configure the parallel computing. When I am trying to compile the getting the following error and attached the compile.msg file. Please help me to install WIEN2K in my system. done. Compile time errors (if any) were: SRC_lapw0/compile.msg:collect2: error: ld returned 1 exit status SRC_lapw0/compile.msg:make[1]: *** [lapw0] Error 1 SRC_lapw0/compile.msg:make: *** [seq] Error 2 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] Problem in wien2k17 installation on remote server
Thank you So much sir. I was facing the problem since from last month. I am sorry to disturb you and as Prof. Laurence Marks replied to me " sory for the excuse " I will never try to use such words again. I am extremely sorry. Thank you again. Now I will learn how to deal with the calculations, If any problem arise you please help me sir. Thanking you Indranil On Sat, Sep 1, 2018 at 6:31 PM Gavin Abo wrote: > You need to install and use BLAS. > > I'm not as familiar with scalapack. I believe that is only needed for a > mpi parallel compile. The mpi is useless for a single computer [ > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg03793.html > , > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09334.html > ]. However, it is better to ask your cluster admin about that if you will > be using mpi parallel, because usually they have a specific scalapack > already installed that you would need to use. > > If you decide to use the operating system openblas and lapack package, I > tried it and it seems to compile just fine using compile settings below: > > username@computername:~$ lsb_release -a > No LSB modules are available. > Distributor ID:Ubuntu > Description:Ubuntu 18.04.1 LTS > Release:18.04 > Codename:bionic > ... > username@computername:~$ sudo apt install liblapack-dev > ... > Do you want to continue? [Y/n] Y > username@computername:~$ sudo apt install libopenblas-dev > ... > username@computername:/usr/include$ ls /usr/lib/x86_64-linux-gnu/lapack/ > liblapack.a liblapack.so liblapack.so.3 liblapack.so.3.7.1 > username@computername:/usr/include$ ls /usr/lib/x86_64-linux-gnu/openblas/ > libblas.a libblas.so libblas.so.3 liblapack.a liblapack.so > liblapack.so.3 > > O Compiler options:-ffree-form -O2 -ffree-line-length-none > L Linker Flags:$(FOPT) > P Preprocessor flags '-DParallel' > R R_LIBS (LAPACK+BLAS):-llapack -lblas -lpthread > On 9/1/2018 12:10 PM, Indranil mal wrote: > > Any specific directory I have to install it or any? > > > Thanking you > Indranil > > > On Sat, Sep 1, 2018 at 11:28 PM Indranil mal > wrote: > >> I have *scalapack-2.0.2 *will it be all right to install or I have to >> follow use BLAS >> > ___ > 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] Problem in wien2k17 installation on remote server
Any specific directory I have to install it or any? Thanking you Indranil On Sat, Sep 1, 2018 at 11:28 PM Indranil mal wrote: > I have *scalapack-2.0.2 *will it be all right to install or I have to > follow use BLAS > > On Sat, Sep 1, 2018 at 5:39 PM Gavin Abo wrote: > >> The compile.msg tells you exactly what is wrong: >> >> error: /opt/libopenblas: No such file or directory >> error: /opt/liblapack: No such file or directory >> >> Using those BLAS and lapack, I don't know. Those might be operating >> systems package ones. Maybe they are not installed [ >> https://askubuntu.com/questions/623578/installing-blas-and-lapack-packages >> ]: >> >> sudo apt-get install libblas-dev liblapack-dev >> >> Or maybe the library filenames are different. Maybe they have to be >> changed to: >> >> R R_LIBS (LAPACK+BLAS):/opt/libopenblas.a /opt/liblapack.a >> -lpthread >> >> However, as I already mentioned, I use: >> >> R R_LIBS (LAPACK+BLAS):-L/home/ubuntu/OpenBLAS-0.2.20 -lopenblas >> -llapack_lapw -lpthread >> >> Where I installed OpenBLAS with [ >> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17175.html >> ]: >> >> ubuntu@ubuntu:~$ cd ~ >> ubuntu@ubuntu:~$ wget >> http://github.com/xianyi/OpenBLAS/archive/v0.2.20.tar.gz >> ... >> ubuntu@ubuntu:~$ tar zxvf v0.2.20.tar.gz >> ... >> ubuntu@ubuntu:~$ cd OpenBLAS-0.2.20/ >> ubuntu@ubuntu:~/OpenBLAS-0.2.20$ make FC=gfortran >> >> On 9/1/2018 11:23 AM, Indranil mal wrote: >> > Thank you for your reply. As I am new in LINUX operating system I >> > could not follow you initially sorry for that. However I am using >> > >> > Ubuntu 18.04.1 LTS >> > Memory 31.3 GiB >> > processor Intel® Core™ i7-7700 CPU @ 3.60GHz × 8 >> > Graphics Intel® HD Graphics 630 (Kaby Lake GT2) >> > GNOME 3.28.2 >> > OS type 64-bit >> > Disk 200.6 GB >> > Please inform me what are the information you need to analyze the >> > errors. I will try to provide you. >> > >> > this time I have used all the recommended options for compiler and >> linker >> > >> > >> > *** >> > * Specify compiler and linker options * >> > *** >> > >> > >> > Recommended options for system linuxgfortran are: >> > Compiler options:-ffree-form -O2 -ffree-line-length-none >> > Linker Flags:$(FOPT) -L../SRC_lib >> > Preprocessor flags: '-DParallel' >> > R_LIB (LAPACK+BLAS): /opt/libopenblas /opt/liblapack -lpthread >> > >> > Current settings: >> > O Compiler options:-ffree-form -O2 -ffree-line-length-none >> > L Linker Flags:$(FOPT) >> > P Preprocessor flags '-DParallel' >> > R R_LIBS (LAPACK+BLAS):/opt/libopenblas /opt/liblapack -lpthread >> > X LIBX options:-DLIBXC -I/opt/etsf/include >> > LIBXC-LIBS: -L/opt/etsf/lib/ -lxcf03 -lxc >> > >> > I have got the attached error while compiling. >> > >> > 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 >> > ___ 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] Problem in wien2k17 installation on remote server
I have *scalapack-2.0.2 *will it be all right to install or I have to follow use BLAS On Sat, Sep 1, 2018 at 5:39 PM Gavin Abo wrote: > The compile.msg tells you exactly what is wrong: > > error: /opt/libopenblas: No such file or directory > error: /opt/liblapack: No such file or directory > > Using those BLAS and lapack, I don't know. Those might be operating > systems package ones. Maybe they are not installed [ > https://askubuntu.com/questions/623578/installing-blas-and-lapack-packages > ]: > > sudo apt-get install libblas-dev liblapack-dev > > Or maybe the library filenames are different. Maybe they have to be > changed to: > > R R_LIBS (LAPACK+BLAS):/opt/libopenblas.a /opt/liblapack.a > -lpthread > > However, as I already mentioned, I use: > > R R_LIBS (LAPACK+BLAS):-L/home/ubuntu/OpenBLAS-0.2.20 -lopenblas > -llapack_lapw -lpthread > > Where I installed OpenBLAS with [ > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17175.html > ]: > > ubuntu@ubuntu:~$ cd ~ > ubuntu@ubuntu:~$ wget > http://github.com/xianyi/OpenBLAS/archive/v0.2.20.tar.gz > ... > ubuntu@ubuntu:~$ tar zxvf v0.2.20.tar.gz > ... > ubuntu@ubuntu:~$ cd OpenBLAS-0.2.20/ > ubuntu@ubuntu:~/OpenBLAS-0.2.20$ make FC=gfortran > > On 9/1/2018 11:23 AM, Indranil mal wrote: > > Thank you for your reply. As I am new in LINUX operating system I > > could not follow you initially sorry for that. However I am using > > > > Ubuntu 18.04.1 LTS > > Memory 31.3 GiB > > processor Intel® Core™ i7-7700 CPU @ 3.60GHz × 8 > > Graphics Intel® HD Graphics 630 (Kaby Lake GT2) > > GNOME 3.28.2 > > OS type 64-bit > > Disk 200.6 GB > > Please inform me what are the information you need to analyze the > > errors. I will try to provide you. > > > > this time I have used all the recommended options for compiler and linker > > > > > > *** > > * Specify compiler and linker options * > > *** > > > > > > Recommended options for system linuxgfortran are: > > Compiler options:-ffree-form -O2 -ffree-line-length-none > > Linker Flags:$(FOPT) -L../SRC_lib > > Preprocessor flags: '-DParallel' > > R_LIB (LAPACK+BLAS): /opt/libopenblas /opt/liblapack -lpthread > > > > Current settings: > > O Compiler options:-ffree-form -O2 -ffree-line-length-none > > L Linker Flags:$(FOPT) > > P Preprocessor flags '-DParallel' > > R R_LIBS (LAPACK+BLAS):/opt/libopenblas /opt/liblapack -lpthread > > X LIBX options:-DLIBXC -I/opt/etsf/include > > LIBXC-LIBS: -L/opt/etsf/lib/ -lxcf03 -lxc > > > > I have got the attached error while compiling. > > > > 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 > ___ 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] Problem in wien2k17 installation on remote server
***
* Specify compiler and linker options *
***
Recommended options for system linuxgfortran are:
Compiler options:-ffree-form -O2 -ffree-line-length-none
Linker Flags:$(FOPT) -L../SRC_lib
Preprocessor flags: '-DParallel'
R_LIB (LAPACK+BLAS): /opt/libopenblas /opt/liblapack -lpthread
Current settings:
O Compiler options:-ffree-form -O2 -ffree-line-length-none
L Linker Flags:$(FOPT)
P Preprocessor flags '-DParallel'
R R_LIBS (LAPACK+BLAS):-Wl,--start-group
${MKLROOT}/lib/intel64/libmkl_gf_lp64.a
${MKLROOT}/lib/intel64/libmkl_gnu_thread.a
${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group -lgomp -lpthread -lm
-ldl
X LIBX options:-DLIBXC -I/opt/etsf/include
LIBXC-LIBS: -L/opt/etsf/lib/ -lxcf03 -lxc
Using the above Configuration I got the attached compile time errors
Thanking you
Indranil
+91 9038059734
On Sat, Sep 1, 2018 at 10:53 PM Indranil mal wrote:
> Thank you for your reply. As I am new in LINUX operating system I could
> not follow you initially sorry for that. However I am using
>
> Ubuntu 18.04.1 LTS
> Memory 31.3 GiB
> processor Intel® Core™ i7-7700 CPU @ 3.60GHz × 8
> Graphics Intel® HD Graphics 630 (Kaby Lake GT2)
> GNOME 3.28.2
> OS type 64-bit
> Disk 200.6 GB
> Please inform me what are the information you need to analyze the errors.
> I will try to provide you.
>
> this time I have used all the recommended options for compiler and linker
>
>
> ***
> * Specify compiler and linker options *
> ***
>
>
> Recommended options for system linuxgfortran are:
> Compiler options:-ffree-form -O2 -ffree-line-length-none
> Linker Flags:$(FOPT) -L../SRC_lib
> Preprocessor flags: '-DParallel'
> R_LIB (LAPACK+BLAS): /opt/libopenblas /opt/liblapack -lpthread
>
> Current settings:
> O Compiler options:-ffree-form -O2 -ffree-line-length-none
> L Linker Flags:$(FOPT)
> P Preprocessor flags '-DParallel'
> R R_LIBS (LAPACK+BLAS):/opt/libopenblas /opt/liblapack -lpthread
> X LIBX options:-DLIBXC -I/opt/etsf/include
> LIBXC-LIBS: -L/opt/etsf/lib/ -lxcf03 -lxc
>
> I have got the attached error while compiling.
>
> Thanking you
> Indranil
>
>
>
>
>
>
> On Sat, Sep 1, 2018 at 4:28 PM Gavin Abo wrote:
>
>> As I previously said, ilp64 is wrong, you should use lp64.
>>
>> Also, with the given information, I doubt anybody can help you. What
>> BLAS and lapack libraries are you using as I don't see which ones you
>> are using in your R_LIBS? What are the compile.msg errors after your
>> BLAS and lapack settings are added to R_LIBS?
>>
>> Regarding Compiler options, I would use "-ffree-form -O2
>> -ffree-line-length-none" (the ones seen as recommended).
>>
>> Regarding Linker Flags, if you are using WIEN2k's lapack, I would leave
>> -L../SRC_lib and add -llapack_lapw to R_LIB like I did in [1]. If you
>> are using an operating system or your own lapack, then I would remove
>> -L../SRC_lib.
>>
>> Regarding Preprocessor flags, looks fine, leave as is.
>>
>> Regarding R_LIBS (LAPACK+BLAS), I would use "/opt/libopenblas
>> /opt/liblapack -lpthread" (the ones seen as recommended). However, I
>> would change "/opt/libopenblas" and "/opt/liblapack" depending on what
>> BLAS and lapack you are using, respectively. As I already mentioned, I
>> use WIEN2k's -llapack_lapw for the lapack. For BLAS, I use OpenBLAS. So
>> I replace "/opt/libopenblas" with "-L/home/username/OpenBLAS-0.2.20
>> -lopenblas" where my user name is ubuntu as you see at [1]. Thus at
>> [1], the R_LIBS settings are:
>>
>> -L/home/ubuntu/OpenBLAS-0.2.20 -lopenblas -llapack_lapw -lpthread
>>
>> Though, if you are using Intel mkl [
>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17339.html
>> ], an operating system, or your own BLAS, you would have to adjust your
>> settings appropriately.
>>
>> Regarding LIBX options and LIBXC-LIBS, looks fine as long as libxc is
>> installed in the directory /opt/etsf (I usually install it in the home
>> directory as seen in [1]).
>>
>> [1]
>> https://
Re: [Wien] Problem in wien2k17 installation on remote server
Thank you for your reply. As I am new in LINUX operating system I could not
follow you initially sorry for that. However I am using
Ubuntu 18.04.1 LTS
Memory 31.3 GiB
processor Intel® Core™ i7-7700 CPU @ 3.60GHz × 8
Graphics Intel® HD Graphics 630 (Kaby Lake GT2)
GNOME 3.28.2
OS type 64-bit
Disk 200.6 GB
Please inform me what are the information you need to analyze the errors. I
will try to provide you.
this time I have used all the recommended options for compiler and linker
***
* Specify compiler and linker options *
***
Recommended options for system linuxgfortran are:
Compiler options:-ffree-form -O2 -ffree-line-length-none
Linker Flags:$(FOPT) -L../SRC_lib
Preprocessor flags: '-DParallel'
R_LIB (LAPACK+BLAS): /opt/libopenblas /opt/liblapack -lpthread
Current settings:
O Compiler options:-ffree-form -O2 -ffree-line-length-none
L Linker Flags:$(FOPT)
P Preprocessor flags '-DParallel'
R R_LIBS (LAPACK+BLAS):/opt/libopenblas /opt/liblapack -lpthread
X LIBX options:-DLIBXC -I/opt/etsf/include
LIBXC-LIBS: -L/opt/etsf/lib/ -lxcf03 -lxc
I have got the attached error while compiling.
Thanking you
Indranil
On Sat, Sep 1, 2018 at 4:28 PM Gavin Abo wrote:
> As I previously said, ilp64 is wrong, you should use lp64.
>
> Also, with the given information, I doubt anybody can help you. What
> BLAS and lapack libraries are you using as I don't see which ones you
> are using in your R_LIBS? What are the compile.msg errors after your
> BLAS and lapack settings are added to R_LIBS?
>
> Regarding Compiler options, I would use "-ffree-form -O2
> -ffree-line-length-none" (the ones seen as recommended).
>
> Regarding Linker Flags, if you are using WIEN2k's lapack, I would leave
> -L../SRC_lib and add -llapack_lapw to R_LIB like I did in [1]. If you
> are using an operating system or your own lapack, then I would remove
> -L../SRC_lib.
>
> Regarding Preprocessor flags, looks fine, leave as is.
>
> Regarding R_LIBS (LAPACK+BLAS), I would use "/opt/libopenblas
> /opt/liblapack -lpthread" (the ones seen as recommended). However, I
> would change "/opt/libopenblas" and "/opt/liblapack" depending on what
> BLAS and lapack you are using, respectively. As I already mentioned, I
> use WIEN2k's -llapack_lapw for the lapack. For BLAS, I use OpenBLAS. So
> I replace "/opt/libopenblas" with "-L/home/username/OpenBLAS-0.2.20
> -lopenblas" where my user name is ubuntu as you see at [1]. Thus at
> [1], the R_LIBS settings are:
>
> -L/home/ubuntu/OpenBLAS-0.2.20 -lopenblas -llapack_lapw -lpthread
>
> Though, if you are using Intel mkl [
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17339.html
> ], an operating system, or your own BLAS, you would have to adjust your
> settings appropriately.
>
> Regarding LIBX options and LIBXC-LIBS, looks fine as long as libxc is
> installed in the directory /opt/etsf (I usually install it in the home
> directory as seen in [1]).
>
> [1]
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17175.html
>
>
> On 9/1/2018 9:45 AM, Indranil mal wrote:
> > I have used LG while configuring the system
> >
> > Could you please tell me what would be the compiler and linker
> > settings for my system. I have used the following
> >
> >
> > Recommended options for system linuxgfortran are:
> > Compiler options:-ffree-form -O2 -ffree-line-length-none
> > Linker Flags:$(FOPT) -L../SRC_lib
> > Preprocessor flags: '-DParallel'
> > R_LIB (LAPACK+BLAS): /opt/libopenblas /opt/liblapack -lpthread
> >
> > Current settings:
> > O Compiler options:-ffree-form -O2 -ffree-line-length-none
> > -fdefault-integer-8 -m64 -I${MKLROOT}/include
> >
> > L Linker Flags: $(FOPT)
> >
> > P Preprocessor flags '-DParallel'
> >
> > R R_LIBS (LAPACK+BLAS):-Wl,--start-group
> > ${MKLROOT}/lib/intel64/libmkl_gf_ilp64.a
> > ${MKLROOT}/lib/intel64/libmkl_gnu_thread.a
> > ${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group -lgomp -lpthread
> > -lm -ldl
> >
> > X LIBX options:-DLIBXC -I/opt/etsf/include
> > LIBXC-LIBS: -L/opt/etsf/lib/ -lxcf03 -lxc
> ___
> Wien mailing list
> Wien@zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
&g
Re: [Wien] Problem in wien2k17 installation on remote server
I have used LG while configuring the system
Could you please tell me what would be the compiler and linker settings for
my system. I have used the following
Recommended options for system linuxgfortran are:
Compiler options:-ffree-form -O2 -ffree-line-length-none
Linker Flags:$(FOPT) -L../SRC_lib
Preprocessor flags: '-DParallel'
R_LIB (LAPACK+BLAS): /opt/libopenblas /opt/liblapack -lpthread
Current settings:
O Compiler options:-ffree-form -O2 -ffree-line-length-none
-fdefault-integer-8 -m64 -I${MKLROOT}/include
L Linker Flags: $(FOPT)
P Preprocessor flags '-DParallel'
R R_LIBS (LAPACK+BLAS):-Wl,--start-group
${MKLROOT}/lib/intel64/libmkl_gf_ilp64.a
${MKLROOT}/lib/intel64/libmkl_gnu_thread.a
${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group -lgomp -lpthread -lm
-ldl
X LIBX options:-DLIBXC -I/opt/etsf/include
LIBXC-LIBS: -L/opt/etsf/lib/ -lxcf03 -lxc
On Sat, Sep 1, 2018 at 2:36 PM Gavin Abo wrote:
> The libmkl_gf_ilp64.a looks wrong [
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg10586.html
> ].
> Since you are using gfortran instead of ifort, did you select "LG" and
> "Your compiler: gfortran" during the install?
>
> If not, you may want to start the install over from the beginning by doing
> [
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17823.html
> ]:
>
> rm WIEN2k_INSTALLDATE
>
> Then, perform the gfortran serial calculation install [
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17175.html
> ].
> - libxc-4.0.4.tar.gz can be replaced by the new libxc-4.2.3.tar.gz [
> http://www.tddft.org/programs/libxc/download/ ]
> - Instead of the 17.1 patches, the 18.2 patches can be used [
> https://github.com/gsabo/WIEN2k-Patches/tree/master/18.2 ]
>
> Add LD_LIBRARY_PATH to libopenblasp.so.0 for your Linux environment [
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17212.html
> ]
>
> On 9/1/2018 5:57 AM, Indranil mal wrote:
>
> Could you please tell me what would be the compiler and linker settings
> for my system. I have used
>
>
> Recommended options for system linuxgfortran are:
> Compiler options:-ffree-form -O2 -ffree-line-length-none
> Linker Flags:$(FOPT) -L../SRC_lib
> Preprocessor flags: '-DParallel'
> R_LIB (LAPACK+BLAS): /opt/libopenblas /opt/liblapack -lpthread
>
> Current settings:
> O Compiler options:-ffree-form -O2 -ffree-line-length-none
> -fdefault-integer-8 -m64 -I${MKLROOT}/include
>
> L Linker Flags: $(FOPT)
>
> P Preprocessor flags '-DParallel'
>
> R R_LIBS (LAPACK+BLAS):-Wl,--start-group
> ${MKLROOT}/lib/intel64/libmkl_gf_ilp64.a
> ${MKLROOT}/lib/intel64/libmkl_gnu_thread.a
> ${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group -lgomp -lpthread -lm
> -ldl
>
> X LIBX options:-DLIBXC -I/opt/etsf/include
> LIBXC-LIBS: -L/opt/etsf/lib/ -lxcf03 -lxc
>
>
> On Sat, Sep 1, 2018 at 4:54 PM Indranil mal
> wrote:
>
>> After compiling with gfortran I got the compile message attached bellow.
>> please help me
>>
>> On Wed, Aug 29, 2018 at 6:34 AM Gavin Abo wrote:
>>
>>> ifort: Command not found <- As it says, it cannot find ifort installed
>>> on your system. When you installed ifort using install_GUI.sh (or
>>> install.sh), did it finish without errors [
>>> https://software.intel.com/en-us/articles/intel-compilers-for-linux-and-mac-os-x-compiler-installation-help
>>> ]? After that finished, did you add the source line for your ifort version
>>> to compilervar.sh to your .bashrc (or compilervar.csh to .cshrc) [
>>> https://software.intel.com/en-us/articles/setting-up-the-build-environment-for-using-intel-c-or-fortran-compilers
>>> ]?
>>>
>>> On 8/28/2018 1:55 PM, Indranil mal wrote:
>>>
>>> I have installed fftw in the directory, where I have installed the
>>> WIEN2k. after ./siteconfig_lapw I have made the compiler and all options as
>>> mentioned in the recomended one but when I have tried the compile I got
>>> error and warnings. In the compile.msg file it was written that "
>>>
>>>
>>>
>>>
>>> *rm -f *.o clean ifort -O1 -FR -mp1 -w -prec_div -pc80 -pad -ip
>>> -DINTEL_VML -traceback -assume buffered_io -I/include -c fminenefitCOA.f
>>> make: ifort: Command not found Makefile:46: recipe for target
>>> 'fminenefitCOA.o' failed *
>>> *make: *** [fminenefitCOA.o] Error 127*"
>>>
>>
Re: [Wien] Problem in wien2k17 installation on remote server
After compiling with gfortran I got the compile message attached bellow. please help me On Wed, Aug 29, 2018 at 6:34 AM Gavin Abo wrote: > ifort: Command not found <- As it says, it cannot find ifort installed on > your system. When you installed ifort using install_GUI.sh (or > install.sh), did it finish without errors [ > https://software.intel.com/en-us/articles/intel-compilers-for-linux-and-mac-os-x-compiler-installation-help > ]? After that finished, did you add the source line for your ifort version > to compilervar.sh to your .bashrc (or compilervar.csh to .cshrc) [ > https://software.intel.com/en-us/articles/setting-up-the-build-environment-for-using-intel-c-or-fortran-compilers > ]? > > On 8/28/2018 1:55 PM, Indranil mal wrote: > > I have installed fftw in the directory, where I have installed the WIEN2k. > after ./siteconfig_lapw I have made the compiler and all options as > mentioned in the recomended one but when I have tried the compile I got > error and warnings. In the compile.msg file it was written that " > > > > > *rm -f *.o clean ifort -O1 -FR -mp1 -w -prec_div -pc80 -pad -ip > -DINTEL_VML -traceback -assume buffered_io -I/include -c fminenefitCOA.f > make: ifort: Command not found Makefile:46: recipe for target > 'fminenefitCOA.o' failed * > *make: *** [fminenefitCOA.o] Error 127*" > > please help me. > > ___ > 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 > compile.msg 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] Problem in wien2k17 installation on remote server
I have installed fftw in the directory, where I have installed the WIEN2k. after ./siteconfig_lapw I have made the compiler and all options as mentioned in the recomended one but when I have tried the compile I got error and warnings. In the compile.msg file it was written that " *rm -f *.ocleanifort -O1 -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -assume buffered_io -I/include -c fminenefitCOA.f make: ifort: Command not foundMakefile:46: recipe for target 'fminenefitCOA.o' failed* *make: *** [fminenefitCOA.o] Error 127*" please help me. On Sat, Aug 25, 2018 at 7:15 PM Gavin Abo wrote: > Where did you install the fftw3 libraries? > > Since mpi calculations need a cluster, sometimes the fftw3 libraries (and > other WIEN2k dependencies) were already installed by the cluster admin > (helpdesk) or a request was sent for fftw3 libraries to the helpdesk for > the cluster and the IT department installed it. Then, the location to the > fftw3 library files that was provided by the helpdesk was used. > > If you happen to need to install fftw3 yourself, the [1] uses the --prefix > in the ./configure command to tell it to install in /opt/fftw3. Others > prefer to use a different install location such as in [2]. > > I, however, use > > --prefix=/home/username/fftw3/ > > so that it matches my fftw3 siteconfig settings seen in my previous post > below (where username I usually have to replace with the user name used > to login to the cluster). > > Though, alternatively, you can change the siteconfig fftw3 settings to > match the --prefix location that you used. > > Also, check the location where the fftw3 library files are installed. Do > the fftw3 library files (libfftw3.a and libfftw3_mpi.a corresponding to > -lfftw3 and -lfftw3_mpi, respectively) exist and have non-zero file sizes? > If not, fftw3 might not have compiled without errors. > > For example, libfftw3.a exists with a file size of 1619484 and > libfftw3_mpi.a has a file size of 157960 on one of my computers (note: > those file sizes may be different on your cluster): > > username@computername:~/Desktop$ ls -l /home/username/fftw3/lib > total 1752 > -rw-r--r-- 1 username username 1619484 Aug 25 06:58 libfftw3.a > -rwxr-xr-x 1 username username 893 Aug 25 06:58 libfftw3.la > -rw-r--r-- 1 username username 157960 Aug 25 06:58 libfftw3_mpi.a > -rwxr-xr-x 1 username username 939 Aug 25 06:58 libfftw3_mpi.la > drwxrwxr-x 2 username username4096 Aug 25 06:58 pkgconfig > > [1] > http://wien2k-algerien1970.blogspot.com/2016/08/how-to-install-version-2014-of-wien2k.html > > [2] > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg03405.html > On 8/25/2018 1:34 AM, Lawal Mohammed wrote: > > Dear Gavin, > > I have tried WIEN2k 18.2, but got may be similar issues in lapw0 and lapw2 > parallel compilation. This time around the errors in both SRC_lapw0/ > compile.msg and SRC_lapw2/compile.msg are: > > ld: cannot find -lfftw3_mpi > ld: cannot find -lfftw3 > > Please how to resolve this problem. > > Thanks for your time. > > Regards > > > *Lawal * > > > On Thursday, August 23, 2018, 8:18:34 PM GMT+8, Gavin Abo > wrote: > > > In WIEN2k 18.2, I have in siteconfig: > >Libraries: > > F FFTW options: -DFFTW3 -I/home/username/fftw3/include > FFTW-LIBS: -L/home/username/fftw3/lib -lfftw3 > FFTW-PLIBS: -lfftw3_mpi > In my SRC_lapw0/compile.msg, I see: > > -DFFTW3 -I/home/username/fftw3/include > > In the /home/username/fftw3/include directory my system, I have the file > fftw3.f03. > > In your SRC_lapw0/compile.msg, I see: > > -I/BIGDATA1/app/intelcompiler/14.0.2/composer_xe_2013_sp1.2.144/mkl/include > -DFFTW3 -I/usr/lib64/include > > Maybe the /usr/lib64/include directory does not have file fftw3.f03. For > serial complication, it should be possible to use the operating system > fftw3 library installed with package manager. However, I don't think it > provided the fftw3 mpi library file (libfftw_mpi.a) such that parallel > compilation would not work with it. The fftw3 library can be download [ > http://www.fftw.org/download.html ] and installed [Refer to "Install the > library fftw3" at > http://wien2k-algerien1970.blogspot.com/2016/08/how-to-install-version-2014-of-wien2k.html > ]. > > Also, I cannot remember for sure, but their may have been some siteconfig > issues with fftw when parallel compiling in 17.1. Those problems should > however be fixed in WIEN2k 18.2. > > ___ > 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:
