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: > > > > 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
Re: [Wien] Using fold2Bloch for the path perpendicular to G-K
Dear Oleg, thank you for your help! Your advice was very useful for me and now my problem is resolved. Over time, I would like to realize an automation of individual selecting the divider for different sectors of the k-path. For example, it will be useful for path consisting points Gamma and M simultaneously (in other case "quality" of GM may be worse than GK). I think, the procedure should be similar to analogous function in xcrysden. Best regards, Artem. ___ 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] impi memory leak
For reference, the impi memory leak which has been present for some years has now been repaired according to my tests, using the 2019 Update 5 version (it may have already have been repaired with Update 4). -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu Corrosion in 4D: www.numis.northwestern.edu/MURI Co-Editor, Acta Cryst A "Research is to see what everybody else has seen, and to think what nobody else has thought" Albert Szent-Gyorgi ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] parallel ssh error
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:
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
>
