Re: [Wien] parallel ssh error

2019-09-30 Thread Gavin Abo 

Good to see.  As you know, "hup: Command not found" can be ignored:

http://zeus.theochem.tuwien.ac.at/pipermail/wien/2011-April/014484.html
http://zeus.theochem.tuwien.ac.at/pipermail/wien/2010-September/013598.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11131.html

On 9/30/2019 10:35 AM, Indranil mal wrote:
Thank you Sir for your instantaneous support. Now it is working 
smoothly only with hup: Command not found

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Re: [Wien] parallel ssh error

2019-09-30 Thread Indranil mal 
 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/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.

Re: [Wien] parallel ssh error

2019-09-30 Thread Gavin Abo 
An additional comment, /home/username/WIEN2k (or ~/WIEN2k) is where I 
have WIEN2k installed.  Whereas, you have installed WIEN2k at 
/servernode1 [1].  In the examples of my previous posts (e.g. [2]) you 
might find some typographical errors were I forget to replace my 
/home/username/WIEN2k with your /servernode1.


It is best to have WIEN2k setup at a common path location on all nodes 
[3,4] (i.e., your vlsi1-vsli4).  Therefore, I recommend to not have 
WIEN2k at other locations among your system nodes like the 
/home/username/WIEN2K as you mentioned below.


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19036.html
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19061.html
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17988.html
[4] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09229.html


On 9/30/2019 12:59 AM, Peter Blaha wrote:
So there is progress as now the environment seems to be accepted in 
the remote shell.


lapw1para (called by x_lapw, which is called by run_lapw -p) creates 
the splitted klists-files (case.klist_1,...) and def files 
lapw1_1.def,...


It uses the $cwd variable and executes basically:

ssh vlsi1 "cd $cwd; lapw1c lapw1_1.def "

Does this work on your computers ?



On 9/29/19 7:16 PM, 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/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

   

Re: [Wien] [Wien2k] help for charge densities calculated from lapw5

2019-09-30 Thread Peter Blaha 

You are using a very old WIEN2k version.

At that time x lapw5 would ALWAYS produce "clmval".

So the ONLY way to produce the total density was to edit lapw5.def and 
case.in5 to set the correct values and then run lapw5 lapw5.def


The latest WIEN2k has several switches (-tot/-pot/-coulomb/-exchange and 
eg.   x lapw5 -tot

does the job.

On 9/30/19 11:17 AM, sha haozhi wrote:

Dear All,

When I calculated charge densities of cubic TiC using lapw5 in WIEN2k 
13.1, I found the valence charge density is bigger than the total charge 
density.


During the calculation, I constructed the case.in5 file first and then 
did ‘x lapw5’. I used ‘VAL’in case.in5 for valence charge density 
calculation and ‘TOT’for total charge density.


Also, I found in both cases, the lapw5.def files are the same as follows:

5 ,'TiC.in5', 'old',    'formatted',0

6 ,'TiC.output5',   'unknown','formatted',0

8 ,'TiC.struct',    'old',    'formatted',0

9 ,'TiC.clmval',    'old',    'formatted',0

10,'TiC.tmp',   'unknown','unformatted',0

11,'TiC.clmvaldn',  'unknown','formatted',0

12,'TiC.sigma', 'unknown','formatted',0

20,'TiC.rho_onedim','unknown','formatted',0

21,'TiC.rho',   'unknown','formatted',0

However, when I used the following steps to get the total charge 
density, the result seemed to be right:


(1)Construct case.in5 file with cnorm=’TOT’.

(2)Construct lapw5.def:

$ x lapw5 -d

(3)Change the ‘case.clmval’in lapw5.def to ‘case.clmsum’.

(4)Do the calculaton:

$ lapw5 lapw5.def

So, I wonder if the steps above are right and how does the lapw5 works ? 
Why the command ‘x lapw5 -d’always generate a lapw5.def with ‘’9, 
‘case.clmval’ ‘’no matter cnorm=’VAL’or ‘TOT’in case.in5 ?


Best regards

Haozhi Sha


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--

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--
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Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
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[Wien] [Wien2k] help for charge densities calculated from lapw5

2019-09-30 Thread sha haozhi 
Dear All,
When I calculated charge densities of cubic TiC using lapw5 in WIEN2k 13.1, I 
found the valence charge density is bigger than the total charge density.
During the calculation, I constructed the case.in5 file first and then did ‘x 
lapw5’. I used ‘VAL’ in case.in5 for valence charge density calculation and 
‘TOT’ for total charge density.
Also, I found in both cases, the lapw5.def files are the same as follows:
5 ,'TiC.in5', 'old','formatted',0
6 ,'TiC.output5',   'unknown','formatted',0
8 ,'TiC.struct','old','formatted',0
9 ,'TiC.clmval','old','formatted',0
10,'TiC.tmp',   'unknown','unformatted',0
11,'TiC.clmvaldn',  'unknown','formatted',0
12,'TiC.sigma', 'unknown','formatted',0
20,'TiC.rho_onedim','unknown','formatted',0
21,'TiC.rho',   'unknown','formatted',0

However, when I used the following steps to get the total charge density, the 
result seemed to be right:

(1)   Construct case.in5 file with cnorm=’TOT’.

(2)   Construct lapw5.def:

$ x lapw5 -d

(3)   Change the ‘case.clmval’ in lapw5.def to ‘case.clmsum’.

(4)   Do the calculaton:

$ lapw5 lapw5.def
So, I wonder if the steps above are right and how does the lapw5 works ? Why 
the command ‘x lapw5 -d’ always generate a lapw5.def with ‘’ 9, ‘case.clmval’ 
‘’ no matter cnorm=’VAL’ or ‘TOT’ in case.in5 ?

Best regards
Haozhi Sha
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Re: [Wien] parallel ssh error

2019-09-30 Thread Peter Blaha 
So there is progress as now the environment seems to be accepted in the 
remote shell.


lapw1para (called by x_lapw, which is called by run_lapw -p) creates the 
splitted klists-files (case.klist_1,...) and def files lapw1_1.def,...


It uses the $cwd variable and executes basically:

ssh vlsi1 "cd $cwd; lapw1c lapw1_1.def "

Does this work on your computers ?



On 9/29/19 7:16 PM, 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/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