Re: [Wien] Parallel calculation

[Gavin Abo]

If you are using gfortran and gcc and it helps, some of the keystrokes I 
captured are shown below from when I installed WIEN2k 21.1.  These are 
just steps I follow as a guide for getting started and for a 
configuration that gets WIEN2k on my system up and running quickly.  
After that, I usually have to go back into ./siteconfig and further 
adjust the settings to make calculations complete faster by finding 
better settings to use for my system in the documentation for the 
compilers.  For example, the gfortran documentation is at [1].  Other 
compilers, like the Intel Fortran compiler [2], should have their own 
documentation.


The mpi parallel settings configured below don't always work depending 
on the configuration that I need on my computer systems.  When that 
happens, the WIEN2k usersguide [3] and FAQ questions page [4] help with 
choosing the correct siteconfig settings.  Or past posts on parallel 
calculations in the mailing list archive contained a solution to the 
issues I encountered.


I haven't tried the SRC_mpiutil on the unsupported page [5] with WIEN2k 
21.1 but I think that was helpful when I looked at that when using a 
past WIEN2k version.


For the below, I used Open MPI [6], but you could use another mpi 
implementation [7].


[1] https://gcc.gnu.org/wiki/GFortran
[2] 
https://software.intel.com/content/www/us/en/develop/documentation/fortran-compiler-oneapi-dev-guide-and-reference/top.html

[3] http://www.wien2k.at/reg_user/textbooks/usersguide.pdf
[4] http://www.wien2k.at/reg_user/faq/pbs.html
[5] http://www.wien2k.at/reg_user/unsupported/
[6] https://www.open-mpi.org/
[7] https://en.wikipedia.org/wiki/MPICH

*Installed Ubuntu LTS*

https://help.ubuntu.com/community/Installation
https://ubuntu.com/#download

username@computername:~$ lsb_release -a
No LSB modules are available.
Distributor ID:    Ubuntu
Description:    Ubuntu 20.04.2 LTS
Release:    20.04
Codename:    focal

*Installed XCrySDen*

username@computername:~$ cd ~
username@computername:~$ sudo apt update
username@computername:~$ sudo apt install tcsh ghostscript octave 
gnuplot gnuplot-x11 make autoconf libtool perl libquadmath0 gfortran 
build-essential libglu1-mesa-dev libtogl-dev tcl-dev tk-dev libfftw3-dev 
libxmu-dev
username@computername:~$ wget 
http://www.xcrysden.org/download/xcrysden-1.6.2.tar.gz

username@computername:~$ tar xvf xcrysden-1.6.2.tar.gz
username@computername:~$ cd xcrysden-1.6.2
username@computername:~/xcrysden-1.6.2$ cp ./system/Make.sys-shared Make.sys
username@computername:~/xcrysden-1.6.2$ make all
username@computername:~/xcrysden-1.6.2$ echo 'export 
XCRYSDEN_TOPDIR=/home/username/xcrysden-1.6.2'>>~/.bashrc
username@computername:~/xcrysden-1.6.2$ echo 'export 
PATH=$PATH:$XCRYSDEN_TOPDIR'>>~/.bashrc

username@computername:~/xcrysden-1.6.2$ source ~/.bashrc

*Installed libxc*

username@computername:~/xcrysden-1.6.2$ cd ~
username@computername:~$ wget 
http://www.tddft.org/programs/libxc/down.php?file=5.1.4/libxc-5.1.4.tar.gz

username@computername:~$ tar xvf down.php\?file\=5.1.4%2Flibxc-5.1.4.tar.gz
username@computername:~$ cd libxc-5.1.4/
username@computername:~/libxc-5.1.4$ autoreconf -i --force
username@computername:~/libxc-5.1.4$ ./configure FC=gfortran CC=gcc 
--prefix=$HOME/libxc-5.1.4

username@computername:~/libxc-5.1.4$ make
username@computername:~/libxc-5.1.4$ make check
username@computername:~/libxc-5.1.4$ make install

*Installed OpenBLAS*

username@computername:~/libxc-5.1.4$ cd ~
username@computername:~$ wget 
https://github.com/xianyi/OpenBLAS/releases/download/v0.3.15/OpenBLAS-0.3.15.tar.gz

username@computername:~$ tar zxvf OpenBLAS-0.3.15.tar.gz
username@computername:~$ cd OpenBLAS-0.3.15/
username@computername:~/OpenBLAS-0.3.15$ make FC=gfortran CC=gcc
username@computername:~/OpenBLAS-0.3.15$ echo 'export 
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/username/OpenBLAS-0.3.15'>>~/.bashrc

username@computername:~/OpenBLAS-0.3.15$ source ~/.bashrc

*Installed Open MPI*

username@computername:~/OpenBLAS-0.3.15$ cd ~
username@computername:~$ wget 
https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.1.tar.gz

username@computername:~$ tar xvf openmpi-4.1.1.tar.gz
username@computername:~$ cd openmpi-4.1.1/
username@computername:~/openmpi-4.1.1$ ./configure 
--prefix=$HOME/openmpi-4.1.1

username@computername:~/openmpi-4.1.1$ make all install
username@computername:~/openmpi-4.1.1$ echo 'export 
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/username/openmpi-4.1.1/lib'>>~/.bashrc
username@computername:~/openmpi-4.1.1$ echo 'export 
PATH=$PATH:/home/username/openmpi-4.1.1/bin'>>~/.bashrc

username@computername:~/openmpi-4.1.1$ source ~/.bashrc

*Installed fftw*

username@computername:~/openmpi-4.1.1$ cd ~
username@computername:~$ wget http://www.fftw.org/fftw-3.3.9.tar.gz
username@computername:~$ tar xvf fftw-3.3.9.tar.gz
username@computername:~$ cd fftw-3.3.9/
username@computername:~/fftw-3.3.9$ ./configure FCC=gfortran CC=gcc 
MPICC=mpicc --enable-mpi --prefix=$HOME/fftw-3.3.9

Re: [Wien] Parallel calculation

[Laurence Marks]

Let's take this step by step.

There are three parallel modes, k-points, open-mp and mpi. For calculations
with 20 atoms or less (roughly) you only need k-points and open-mp. Open-mp
is installed as part of your compile options. Please read the user guide.

For mpi you need a fast connection, and mpi installed (openmpi, Intel or
other). Then it is configurable in the compile.

What do you have, and what are you trying to do, your question was way too
open.

_
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Györgyi
www.numis.northwestern.edu

On Tue, Jun 8, 2021, 07:21 ben amara imen  wrote:

> Dear
>
> Can someone tell me how I can install the parallel calculation for Wien2k .
> Thanks in advance
>
>
> Best regards
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[Wien] Parallel calculation

[ben amara imen]

Dear

Can someone tell me how I can install the parallel calculation for Wien2k .
Thanks in advance


Best regards
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Re: [Wien] Parallel calculation in more than 2 nodes

[Laurence Marks]

parallel_options is sourced by all the mpi scripts, so you don't want to
edit lapw1para or any of the others. It should now work for everything.

_
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 Wed, Jul 22, 2020, 03:48 MA Weiliang  wrote:

> Hi,
>
> I changed the parallel_option with ' setenv WIEN_MPIRUN "mpirun -np _NP_
> -machinefile _HOSTS_ _EXEC_” '. It works.
>
> There are some lines in lapw1para_lapw, so I just tried to comment the
> MPIRUN lines in parallel_options before.
>
> if ( $?WIEN_MPIRUN ) then
>   set mpirun = "$WIEN_MPIRUN"
> else
>   set mpirun='mpirun -np _NP_ _EXEC_'
> endif
>
>
> Thank you again.
>
> Best regards,
> Weiliang MA
>
>
>
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Re: [Wien] Parallel calculation in more than 2 nodes

[MA Weiliang]

Hi, 

I changed the parallel_option with ' setenv WIEN_MPIRUN "mpirun -np _NP_ 
-machinefile _HOSTS_ _EXEC_” '. It works.

There are some lines in lapw1para_lapw, so I just tried to comment the MPIRUN 
lines in parallel_options before. 

if ( $?WIEN_MPIRUN ) then
  set mpirun = "$WIEN_MPIRUN"
else
  set mpirun='mpirun -np _NP_ _EXEC_'
endif


Thank you again.

Best regards,
Weiliang MA



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Re: [Wien] Parallel calculation in more than 2 nodes

[Peter Blaha]

> parallel option file: # setenv WIEN_MPIRUN "srun -K1 _EXEC_"
> Because of compatible issues, we don't use srun by commented the
> WIEN_MPIRUN line in parallel option file and use the mpirun directly.

You cannot just comment the MPIRUN variable,
but if you don't want to use srun you should set it to:

setenv WIEN_MPIRUN "mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_"

(or use during siteconfig the option of ifort (without srun))

Regards

On 7/21/20 12:48 PM, MA Weiliang wrote:

Dear WIEN2K users,

The cluster we used is a memory shared system with 16 cpus per node. The 
calculation distributed in 2 nodes with 32 cpus. But actually all the mpi 
processes were running in the first node according to the attached top ouput. 
There were not processes in the second nodes.  As you can see, the usage of cpu 
is around 50%. It seemes that the calculation didn't distribute in 2 nodes, but 
only splitted the fisrt node (16 cpus) into 32 prcesses with half computing 
power.

Do you have any ideas for this problem? The .machines, wien2k info, dayfile and 
job output are attached below. Thank you!

Best,
Weiliang


##
#  output of top
##
   PID USER PR  NI  VIRT  RES  SHR S %CPU %MEMTIME+  COMMAND
43504 mc20   0  614m 262m  27m R 50.2  0.3  21:45.54 lapw1c_mpi
43507 mc20   0  611m 259m  26m R 50.2  0.3  21:50.76 lapw1c_mpi
43514 mc20   0  614m 255m  22m R 50.2  0.3  21:51.37 lapw1c_mpi
...
32 lines in total
...
43508 mc20   0  615m 260m  23m R 49.5  0.3  21:43.73 lapw1c_mpi
43513 mc20   0  616m 257m  22m R 49.5  0.3  21:51.32 lapw1c_mpi
43565 mc20   0  562m 265m  24m R 49.5  0.3  21:43.29 lapw1c_mpi


##
# .machines file
##
1:lame26:16
1:lame28:16
lapw0: lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 
lame26 lame26 lame26 lame26 lame26 lame26 lame28 lame28 lame28 lame28 lame28 
lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28
dstart: lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 
lame26 lame26 lame26 lame26 lame26 lame26 lame28 lame28 lame28 lame28 lame28 
lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28
nlvdw: lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 
lame26 lame26 lame26 lame26 lame26 lame26 lame28 lame28 lame28 lame28 lame28 
lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28
lapw2_vector_split:2
granularity:1
extrafine:1


##
# wien2k info
##
wien2k version: 18.2
complier: ifort, icc, mpiifort (intel 2017 compliers)
parallel option file: # setenv WIEN_MPIRUN "srun -K1 _EXEC_"
Because of compatible issues, we don't use srun by commented the WIEN_MPIRUN 
line in parallel option file and use the mpirun directly.


##
# dayfile
##
 cycle 7 (Mon Jul 20 20:56:01 CEST 2020) (194/93 to go)


   lapw0  -p   (20:56:01) starting parallel lapw0 at Mon Jul 20 20:56:01 CEST 
2020

 .machine0 : 32 processors
0.087u 0.176s 0:17.87 1.3%  0+0k 0+112io 0pf+0w

   lapw1  -p   -c  (20:56:19) starting parallel lapw1 at Mon Jul 20 
20:56:19 CEST 2020

->  starting parallel LAPW1 jobs at Mon Jul 20 20:56:20 CEST 2020
running LAPW1 in parallel mode (using .machines)
2 number_of_parallel_jobs
  lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 
lame26 lame26 lame26 lame26 lame26 lame26(16) 0.022u 0.049s 56:37.88 0.0%
 0+0k 0+8io 0pf+0w
  lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 
lame28 lame28 lame28 lame28 lame28 lame28(16) 0.031u 0.038s 56:00.24 0.0%
 0+0k 0+8io 0pf+0w
Summary of lapw1para:
lame26k=0 user=0  wallclock=0
lame28k=0 user=0  wallclock=0
18.849u 18.501s 56:40.85 1.0%   0+0k 0+1032io 0pf+0w

   lapwso -p -c(21:53:00) running LAPWSO in parallel mode

   lame26 0.026u 0.044s 2:20:06.55 0.0% 0+0k 0+8io 0pf+0w
   lame28 0.027u 0.043s 2:18:40.89 0.0% 0+0k 0+8io 0pf+0w
Summary of lapwsopara:
lame26user=0.026  wallclock=140
lame28user=0.027  wallclock=138
0.235u 2.621s 2:20:13.57 0.0%   0+0k 0+864io 0pf+0w

   lapw2 -p-c -so  (00:13:14) running LAPW2 in parallel mode

   lame26 0.023u 0.044s 4:58.20 0.0% 0+0k 0+8io 0pf+0w
   lame28 0.024u 0.044s 5:02.58 0.0% 0+0k 0+8io 0pf+0w
Summary of lapw2para:
lame26user=0.023  wallclock=298.2
lame28user=0.024  wallclock=302.58
5.836u 1.057s 5:11.94 2.2%  0+0k 0+166184io 0pf+0w

   lcore   (00:18:26) 1.576u 0.042s 0:02.06 78.1%  0+0k 0+12888io 0pf+0w
   mixer   (00:18:30) 6.472u 0.687s 0:07.97 89.7%  0+0k 0+308832io 0pf+0w

:ENERGY 

Re: [Wien] Parallel calculation in more than 2 nodes

[MA Weiliang]

Parallel_option:

setenv TASKSET "no"
if ( ! $?USE_REMOTE ) setenv USE_REMOTE 0
if ( ! $?MPI_REMOTE ) setenv MPI_REMOTE 0
setenv WIEN_GRANULARITY 1
setenv DELAY 0.1
setenv SLEEPY 1
#setenv WIEN_MPIRUN "srun -K1 _EXEC_"
if ( ! $?CORES_PER_NODE) setenv CORES_PER_NODE  16
#if ( ! $?PINNING_COMMAND) setenv PINNING_COMMAND "--cpu_bind=map_cpu:"
#if ( ! $?PINNING_LIST ) setenv PINNING_LIST 
“0,8,1,9,2,10,3,11,4,12,5,13,6,14,7,15"

mpi:  mpirun in intel 2017 compliers.


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Re: [Wien] Parallel calculation in more than 2 nodes

[Laurence Marks]

i.e. paste the result of "cat $WIENROOT/parallel_options" into an email.

_
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 Tue, Jul 21, 2020, 07:44 Laurence Marks  wrote:

> What are you using in parallel_options? The statement:
> "parallel option file: # setenv WIEN_MPIRUN "srun -K1 _EXEC_"
> Because of compatible issues, we don't use srun by commented the
> WIEN_MPIRUN line in parallel option file and use the mpirun directly." is
> ambiguous.
>
> What mpi?
> _
> 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 Tue, Jul 21, 2020, 05:48 MA Weiliang 
> wrote:
>
>> Dear WIEN2K users,
>>
>> The cluster we used is a memory shared system with 16 cpus per node. The
>> calculation distributed in 2 nodes with 32 cpus. But actually all the mpi
>> processes were running in the first node according to the attached top
>> ouput. There were not processes in the second nodes.  As you can see, the
>> usage of cpu is around 50%. It seemes that the calculation didn't
>> distribute in 2 nodes, but only splitted the fisrt node (16 cpus) into 32
>> prcesses with half computing power.
>>
>> Do you have any ideas for this problem? The .machines, wien2k info,
>> dayfile and job output are attached below. Thank you!
>>
>> Best,
>> Weiliang
>>
>>
>> ##
>> #  output of top
>> ##
>>   PID USER PR  NI  VIRT  RES  SHR S %CPU %MEMTIME+  COMMAND
>> 43504 mc20   0  614m 262m  27m R 50.2  0.3  21:45.54 lapw1c_mpi
>> 43507 mc
>>
>> granularity:1
>> extrafine:1
>>
>>
>> ##
>> # wien2k info
>> ##
>> wien2k version: 18.2
>> complier: ifort, icc, mpiifort (intel 2017 compliers)
>> parallel option file: # setenv WIEN_MPIRUN "srun -K1 _EXEC_"
>> Because of compatible issues, we don't use srun by commented the
>> WIEN_MPIRUN line in parallel option file and use the mpirun directly.
>>
>>
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>>
>
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Re: [Wien] Parallel calculation in more than 2 nodes

[Laurence Marks]

What are you using in parallel_options? The statement:
"parallel option file: # setenv WIEN_MPIRUN "srun -K1 _EXEC_"
Because of compatible issues, we don't use srun by commented the
WIEN_MPIRUN line in parallel option file and use the mpirun directly." is
ambiguous.

What mpi?
_
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 Tue, Jul 21, 2020, 05:48 MA Weiliang  wrote:

> Dear WIEN2K users,
>
> The cluster we used is a memory shared system with 16 cpus per node. The
> calculation distributed in 2 nodes with 32 cpus. But actually all the mpi
> processes were running in the first node according to the attached top
> ouput. There were not processes in the second nodes.  As you can see, the
> usage of cpu is around 50%. It seemes that the calculation didn't
> distribute in 2 nodes, but only splitted the fisrt node (16 cpus) into 32
> prcesses with half computing power.
>
> Do you have any ideas for this problem? The .machines, wien2k info,
> dayfile and job output are attached below. Thank you!
>
> Best,
> Weiliang
>
>
> ##
> #  output of top
> ##
>   PID USER PR  NI  VIRT  RES  SHR S %CPU %MEMTIME+  COMMAND
> 43504 mc20   0  614m 262m  27m R 50.2  0.3  21:45.54 lapw1c_mpi
> 43507 mc
>
> granularity:1
> extrafine:1
>
>
> ##
> # wien2k info
> ##
> wien2k version: 18.2
> complier: ifort, icc, mpiifort (intel 2017 compliers)
> parallel option file: # setenv WIEN_MPIRUN "srun -K1 _EXEC_"
> Because of compatible issues, we don't use srun by commented the
> WIEN_MPIRUN line in parallel option file and use the mpirun directly.
>
>
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[Wien] Parallel calculation in more than 2 nodes

[MA Weiliang]

Dear WIEN2K users,

The cluster we used is a memory shared system with 16 cpus per node. The 
calculation distributed in 2 nodes with 32 cpus. But actually all the mpi 
processes were running in the first node according to the attached top ouput. 
There were not processes in the second nodes.  As you can see, the usage of cpu 
is around 50%. It seemes that the calculation didn't distribute in 2 nodes, but 
only splitted the fisrt node (16 cpus) into 32 prcesses with half computing 
power. 

Do you have any ideas for this problem? The .machines, wien2k info, dayfile and 
job output are attached below. Thank you!

Best,
Weiliang


##
#  output of top
##
  PID USER PR  NI  VIRT  RES  SHR S %CPU %MEMTIME+  COMMAND
43504 mc20   0  614m 262m  27m R 50.2  0.3  21:45.54 lapw1c_mpi
43507 mc20   0  611m 259m  26m R 50.2  0.3  21:50.76 lapw1c_mpi
43514 mc20   0  614m 255m  22m R 50.2  0.3  21:51.37 lapw1c_mpi
...
32 lines in total
...   
43508 mc20   0  615m 260m  23m R 49.5  0.3  21:43.73 lapw1c_mpi
43513 mc20   0  616m 257m  22m R 49.5  0.3  21:51.32 lapw1c_mpi
43565 mc20   0  562m 265m  24m R 49.5  0.3  21:43.29 lapw1c_mpi 


##
# .machines file
##
1:lame26:16
1:lame28:16
lapw0: lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 
lame26 lame26 lame26 lame26 lame26 lame26 lame28 lame28 lame28 lame28 lame28 
lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28
dstart: lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 
lame26 lame26 lame26 lame26 lame26 lame26 lame28 lame28 lame28 lame28 lame28 
lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28
nlvdw: lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 
lame26 lame26 lame26 lame26 lame26 lame26 lame28 lame28 lame28 lame28 lame28 
lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28
lapw2_vector_split:2
granularity:1
extrafine:1


##
# wien2k info
##
wien2k version: 18.2
complier: ifort, icc, mpiifort (intel 2017 compliers)
parallel option file: # setenv WIEN_MPIRUN "srun -K1 _EXEC_"
Because of compatible issues, we don't use srun by commented the WIEN_MPIRUN 
line in parallel option file and use the mpirun directly.


##
# dayfile
##
cycle 7 (Mon Jul 20 20:56:01 CEST 2020) (194/93 to go)

>   lapw0  -p   (20:56:01) starting parallel lapw0 at Mon Jul 20 20:56:01 CEST 
> 2020
 .machine0 : 32 processors
0.087u 0.176s 0:17.87 1.3%  0+0k 0+112io 0pf+0w
>   lapw1  -p   -c  (20:56:19) starting parallel lapw1 at Mon Jul 20 
> 20:56:19 CEST 2020
->  starting parallel LAPW1 jobs at Mon Jul 20 20:56:20 CEST 2020
running LAPW1 in parallel mode (using .machines)
2 number_of_parallel_jobs
 lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 lame26 
lame26 lame26 lame26 lame26 lame26 lame26(16) 0.022u 0.049s 56:37.88 0.0%
0+0k 0+8io 0pf+0w
 lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 lame28 
lame28 lame28 lame28 lame28 lame28 lame28(16) 0.031u 0.038s 56:00.24 0.0%
0+0k 0+8io 0pf+0w
   Summary of lapw1para:
   lame26k=0 user=0  wallclock=0
   lame28k=0 user=0  wallclock=0
18.849u 18.501s 56:40.85 1.0%   0+0k 0+1032io 0pf+0w
>   lapwso -p -c(21:53:00) running LAPWSO in parallel mode
  lame26 0.026u 0.044s 2:20:06.55 0.0% 0+0k 0+8io 0pf+0w
  lame28 0.027u 0.043s 2:18:40.89 0.0% 0+0k 0+8io 0pf+0w
   Summary of lapwsopara:
   lame26user=0.026  wallclock=140
   lame28user=0.027  wallclock=138
0.235u 2.621s 2:20:13.57 0.0%   0+0k 0+864io 0pf+0w
>   lapw2 -p-c -so  (00:13:14) running LAPW2 in parallel mode
  lame26 0.023u 0.044s 4:58.20 0.0% 0+0k 0+8io 0pf+0w
  lame28 0.024u 0.044s 5:02.58 0.0% 0+0k 0+8io 0pf+0w
   Summary of lapw2para:
   lame26user=0.023  wallclock=298.2
   lame28user=0.024  wallclock=302.58
5.836u 1.057s 5:11.94 2.2%  0+0k 0+166184io 0pf+0w
>   lcore   (00:18:26) 1.576u 0.042s 0:02.06 78.1%  0+0k 0+12888io 0pf+0w
>   mixer   (00:18:30) 6.472u 0.687s 0:07.97 89.7%  0+0k 0+308832io 0pf+0w
:ENERGY convergence:  0 0.05 .000121525000
:CHARGE convergence:  0 0.5 .0002538
ec cc and fc_conv 0 0 1


##
# job output
##
in cycle 3ETEST: .52305136   CTEST: .0049036
 LAPW0 END
[1]Done  mpirun -np 32 
/home/mcs/work/wma/Package/wien2k.18m/lapw0_mpi lapw0.def >> .time00
 LAPW1 END
[1]  - Done

Re: [Wien] Parallel calculation -stop of iterations after mixer. :ENE NaN value

[Laurence Marks]

A NaN means that something has gone wrong. While this may show up with the
mixer, it probably occurs somewhere else. When I look at your struct file,
the Mg and O atoms at the interface have low BVS, indicating that there
will be a significant contraction along your z axis. You picked RMTs for
the initial structure with the spheres almost touching or even touching --
they are smaller than setrmt recommends.

I strongly suspect that your calculation is failing because you have
touching spheres.

The simplest thing to do is reduce the RMTs, for instance use "setrmt case
-r 5". With the previous converged calculation you might be able to use
"reduce_rmt_lapw -r 5 -sp". However, since your initial RMTs were too large
this might not work. Make sure that you do not do this with densities where
you have a NaN.

This may not resolve the problem. I am 99% certain you won't get anywhere
with what you sent with your current RMTs



On Sun, Oct 28, 2018 at 8:36 AM Coriolan TIUSAN <
coriolan.tiu...@phys.utcluj.ro> wrote:

> Dear wien2k users,
>
> I am running wien 18.2 on Ubuntu 18.04 , installed on a HP station:
> 64GB,  Intel® Xeon(R) Gold 5118 CPU @ 2.30GHz × 48.
>
> The fortran compiler/math library are ifc and intel mkl library. For
> parallel execution I have MPI+SCALAPACK, FFTW.
>
> When calculating multilayered structures (e.g. V(3ML)/Fe(3ML)/MgO(3ML)
> in supercell slab model (attached structure file), after a certain
> number of iterations towards the convergence, I have a sudden stop,
> without any error (in error files) after the mixer.
>
> I have similar problems for similar heterostructures: Au/Fe/MgO, but
> only when trying to do geometrical optimization (force minimisation).
> The initial scf calculation for Au/Fe/MgO slab converged (runsp_lapw -cc
> 0.001, -ec 0.0001 -p)  without any errors. I guess that, this would
> demonstrate that the programs have been properly installed and functional?
>
> Coming back to the stop in scf for V/Fe/MgO, the following things can be
> remarked:
>
> 1/ For the  last iteration case.scf file containes NaN values for  :DIS
> and :ENE,
>
> :DEN  : DENSITY INTEGRAL  =NaN   (Ry)
>
> :ENE  : *WARNING** TOTAL ENERGY IN Ry =   NaN
>
> 2/ The dayfile displays:
>
>   LAPW0 END
> [1]Done  mpirun -np 48 -machinefile
> .machine0 /home/tiusan/W2k/lapw0_mpi lapw0.def >> .time00
>   LAPW1 END
> [1]  + Done  ( cd $PWD; $t $ttt; rm -f
> .lock_$lockfile[$p] ) >> .time1_$loop
>   LAPW1 END
> [1]  + Done  ( cd $PWD; $t $ttt; rm -f
> .lock_$lockfile[$p] ) >> .time1_$loop
> LAPW2 - FERMI; weights written
>   LAPW2 END
> [1]Done  ( cd $PWD; $t $ttt $vector_split;
> rm -f .lock_$lockfile[$p] ) >> .time2_$loop
>   SUMPARA END
> LAPW2 - FERMI; weights written
>   LAPW2 END
> [1]Done  ( cd $PWD; $t $ttt $vector_split;
> rm -f .lock_$lockfile[$p] ) >> .time2_$loop
>   SUMPARA END
>   CORE  END
>   CORE  END
>   MIXER END
> (standard_in) 1: syntax error
> (standard_in) 1: syntax error
> (standard_in) 1: syntax error
> (standard_in) 1: syntax error
> (standard_in) 1: syntax error
> etest: Subscript out of range.
>
> 3/ Following some remarks from the frum, I have added sleep 1 in the
> testconv script, without any success...
>
> Could someone help?
>
> With thanks in advance,
>
> Coriolan TIUSAN
>
>
>
> --
> __
> |   Prof. Dr. Eng. Habil. Coriolan Viorel TIUSAN  |
> |---  |
> | |
> | Department of Physics and Chemistry |
> | Technical University of Cluj-Napoca |
> | |
> | Center of Superconductivity, Spintronics and Surface Science|
> | Str. Memorandumului No. 28, RO-400114 Cluj-Napoca, ROMANIA  |
> | |
> |   Tel: +40-264-401-465 Fax: +40-264-592-055 |
> |Cell: +40-732-893-750|
> |   e-mail: coriolan.tiu...@phys.utcluj.ro|
> |   web:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.c4s.utcluj.ro_=DwIDaQ=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0=gK1X21ldrBrldjPvKy6UgGo_7lxghPbF8Yr2tJYqacU=tkRhrdmNBQuLJiyt8vPw_QlJD2SiWa8vcPMREiRgPh4=
>   |
> |___  |
> | |
> |  Senior Researcher  |
> |  National Center of Scientific Research - FRANCE|
> |  e-mail: coriolan.tiu...@ijl.nancy-universite.fr

[Wien] Parallel calculation -stop of iterations after mixer. :ENE NaN value

[Coriolan TIUSAN]

Dear wien2k users,

I am running wien 18.2 on Ubuntu 18.04 , installed on a HP station: 
64GB,  Intel® Xeon(R) Gold 5118 CPU @ 2.30GHz × 48.


The fortran compiler/math library are ifc and intel mkl library. For 
parallel execution I have MPI+SCALAPACK, FFTW.


When calculating multilayered structures (e.g. V(3ML)/Fe(3ML)/MgO(3ML) 
in supercell slab model (attached structure file), after a certain 
number of iterations towards the convergence, I have a sudden stop, 
without any error (in error files) after the mixer.


I have similar problems for similar heterostructures: Au/Fe/MgO, but 
only when trying to do geometrical optimization (force minimisation). 
The initial scf calculation for Au/Fe/MgO slab converged (runsp_lapw -cc 
0.001, -ec 0.0001 -p)  without any errors. I guess that, this would 
demonstrate that the programs have been properly installed and functional?


Coming back to the stop in scf for V/Fe/MgO, the following things can be 
remarked:


1/ For the  last iteration case.scf file containes NaN values for  :DIS 
and :ENE,


:DEN  : DENSITY INTEGRAL  =    NaN   (Ry)

:ENE  : *WARNING** TOTAL ENERGY IN Ry =   NaN

2/ The dayfile displays:

 LAPW0 END
[1]    Done  mpirun -np 48 -machinefile 
.machine0 /home/tiusan/W2k/lapw0_mpi lapw0.def >> .time00

 LAPW1 END
[1]  + Done  ( cd $PWD; $t $ttt; rm -f 
.lock_$lockfile[$p] ) >> .time1_$loop

 LAPW1 END
[1]  + Done  ( cd $PWD; $t $ttt; rm -f 
.lock_$lockfile[$p] ) >> .time1_$loop

LAPW2 - FERMI; weights written
 LAPW2 END
[1]    Done  ( cd $PWD; $t $ttt $vector_split; 
rm -f .lock_$lockfile[$p] ) >> .time2_$loop

 SUMPARA END
LAPW2 - FERMI; weights written
 LAPW2 END
[1]    Done  ( cd $PWD; $t $ttt $vector_split; 
rm -f .lock_$lockfile[$p] ) >> .time2_$loop

 SUMPARA END
 CORE  END
 CORE  END
 MIXER END
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error
etest: Subscript out of range.

3/ Following some remarks from the frum, I have added sleep 1 in the 
testconv script, without any success...


Could someone help?

With thanks in advance,

Coriolan TIUSAN



--
__
|   Prof. Dr. Eng. Habil. Coriolan Viorel TIUSAN  |
|---  |
| |
| Department of Physics and Chemistry |
| Technical University of Cluj-Napoca |
| |
| Center of Superconductivity, Spintronics and Surface Science|
| Str. Memorandumului No. 28, RO-400114 Cluj-Napoca, ROMANIA  |
| |
|   Tel: +40-264-401-465 Fax: +40-264-592-055 |
|Cell: +40-732-893-750|
|   e-mail: coriolan.tiu...@phys.utcluj.ro|
|   web: http://www.c4s.utcluj.ro/|
|___  |
| |
|  Senior Researcher  |
|  National Center of Scientific Research - FRANCE|
|  e-mail: coriolan.tiu...@ijl.nancy-universite.fr|
|  web: http://www.c4s.utcluj.ro/webperso/tiusan/welcome.html |
|_|

VFeMgO 
P   LATTICE,NONEQUIV.ATOMS: 13 
MODE OF CALC=RELA unit=ang 
  5.725872  5.725872 33.391474 90.00 90.00 90.00   
ATOM  -1: X=0. Y=0. Z=0.
  MULT= 1  ISPLIT=-2
V 1NPT=  781  R0=0.5000 RMT=2.0800   Z: 23.0   
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
ATOM  -2: X=0.5000 Y=0.5000 Z=0.08573854
  MULT= 1  ISPLIT=-2
V 2NPT=  781  R0=0.5000 RMT=2.0800   Z: 23.0   
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
ATOM  -3: X=0. Y=0. Z=0.17147708
  MULT= 1  ISPLIT=-2
V 3NPT=  781  R0=0.5000 RMT=2.0800   Z: 23.0   
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 

[Wien] parallel calculation with 1 kpoint

[Peter Blaha]

Via the mpi-parallel option.

You need a corresponding hardware (MORE than just 4 cores, eg. a cluster with
infiniband), and the corresponding mpi-software.

Read the UG for more details.

Am 16.01.2012 13:28, schrieb ali ghafari:
 Dear Wien2k users

 How can I do parallel calculations with 1 kpoint?

 Best wishes
 Ali


 ___
 Wien mailing list
 Wien at zeus.theochem.tuwien.ac.at
 http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien

-- 

   P.Blaha
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: blaha at theochem.tuwien.ac.atWWW: http://info.tuwien.ac.at/theochem/
--

[Wien] parallel calculation with 1 kpoint

[ali ghafari]

Dear Wien2k users

How can I do parallel calculations with 1 kpoint?

Best wishes
Ali
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[Wien] Parallel calculation with Dual Quad Core

[马超]

Hi Gerhard,  
   
Thank you very much.   
I just changed the environment variables OMP_NUM_THREADS = 8 in bashrc, so all 
processors are used. thanks,   
   
Chao
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[Wien] Parallel calculation with Dual Quad Core Processors

[马超]

Dear Prof. Marks,  
   
Thanks very much for your suggestions. Now, I know how to set up the parallel 
calculation and edit .machines.   
   
In addition, I have another question about the performance of my machine with 
Dual Quad Core Processors (i. e. 8 CPUs). By checking the process, I found 
eight CPUs of my machine were all used by more than 90%, even when I performed 
the calculation without k-point parallelization. I have compared these two 
cases with and without k-point parallelization, and found that they almost took 
the same time. So, I think it is not necessary to perform k-point parallel 
calculation in my case, and that this workstation will automatically allocate 
the mission on average to all eight CPUs . Is my understanding right? Thanks,  
   
Best regards,  
   
Chao
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[Wien] Parallel calculation with Dual Quad Core Processors

[Gerhard Fecher]

Do you use the serial or the parallel version of the MKL ?
The MKL that is used for matrix operations is internally parllelized, the 
behaviour is
usually controlled by the environment variables OMP_NUM_THREADS or 
MKL_NUM_THREADS
as well as some other MKL rlated ones (check the MKL manual).
The use of the parallel MKL may therefore cause that all of youre cores are 
used.
Usually the Wien2k config script sets OMP_NUM_THREADS=1 in the bash.rc,
If you do not figure out what was setting the thread number for the MKL, try to 
force that Wien2k uses the serial version (check the compiler and linker options
in the Intel manuals)

Indeed the use of sveral threads for the mkl and k-point parallelization may be 
contraproductive and can even slow down the program
Note if you change the number of threads using OMP_NUM_THREADS=1, you may need 
to restart W2WEB, otherwise it stays
with the old value.

Ciao
Gerhard


Dr. Gerhard H. Fecher
Institut of Inorganic and Analytical Chemistry
Johannes Gutenberg - University
55099 Mainz

Von: wien-bounces at zeus.theochem.tuwien.ac.at [wien-bounces at 
zeus.theochem.tuwien.ac.at] im Auftrag von ?? [cma at blem.ac.cn]
Gesendet: Sonntag, 10. Januar 2010 00:32
An: wien at zeus.theochem.tuwien.ac.at
Betreff: Re: [Wien] Parallel calculation with Dual Quad Core Processors

Dear Prof. Marks,

Thanks very much for your suggestions. Now, I know how to set up the parallel 
calculation and edit .machines.

In addition, I have another question about the performance of my machine with 
Dual Quad Core Processors (i. e. 8 CPUs). By checking the process, I found 
eight CPUs of my machine were all used by more than 90%, even when I performed 
the calculation without k-point parallelization. I have compared these two 
cases with and without k-point parallelization, and found that they almost took 
the same time. So, I think it is not necessary to perform k-point parallel 
calculation in my case, and that this workstation will automatically allocate 
the mission on average to all eight CPUs . Is my understanding right? Thanks,

Best regards,

Chao

[Wien] Parallel calculation with Dual Quad Core Processors

[马超]

 

Dear All,  

   

I installed Wien2k_09.2 in a workstation with Dual Quad Core Intel Xeon 
Processors. For parallel calculation, can the system automatically allocate the 
k-points to two processors, or, should I edit .machines? If so, How to edit 
.machines? Any suggestion is greatly appreciated.  

   

Best regards,  

Chao Ma
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[Wien] Parallel calculation with Dual Quad Core Processors

[Laurence Marks]

You have to edit .machines -- please read the UG.

2010/1/4 ?? cma at blem.ac.cn:
 Dear All,



 I installed Wien2k_09.2 in?a workstation with Dual Quad Core Intel Xeon
 Processors. For parallel calculation, can the system automatically allocate
 the k-points to two processors, or, should I edit .machines? If so, How to
 edit .machines? Any suggestion is greatly appreciated.



 Best regards,

 Chao Ma

 ___
 Wien mailing list
 Wien at zeus.theochem.tuwien.ac.at
 http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien





-- 
Laurence Marks
Department of Materials Science and Engineering
MSE Rm 2036 Cook Hall
2220 N Campus Drive
Northwestern University
Evanston, IL 60208, USA
Tel: (847) 491-3996 Fax: (847) 491-7820
email: L-marks at northwestern dot edu
Web: www.numis.northwestern.edu
Chair, Commission on Electron Crystallography of IUCR
www.numis.northwestern.edu/
Electron crystallography is the branch of science that uses electron
scattering and imaging to study the structure of matter.

[Wien] parallel calculation stops waiting for a pass in ssh root@localhost

[Ricardo Faccio]

Dear Wien users

I have some problems in using parallelization over kpoints in the latest 
release of WIEN2k. It is important to mention that I had no troubles in the 
past with my settings.

In particular I am working with dual-core pc desktops, and one Quad-core 
machines, individually. For instance, in a simple parallel setup, the typical 
test_case, I found this:

-

root at rfaccio:/home/rfaccio/calculo/wien2k/test_case# x lapw1 -c -up -p

starting parallel lapw1 at Thu Oct  1 23:32:56 UYT 2009

-  starting parallel LAPW1 jobs at Thu Oct  1 23:32:56 UYT 2009

running LAPW1 in parallel mode (using .machines)

2 number_of_parallel_jobs

[1] 30629

root at localhost's password:

-

As you can see the code keeps waiting for my password. It never happened 
before, and it seems to have no relationship with the shared memory setup 
because I used the same flags than in previous release versions.

I use this .machine file:

1:localhost

1:localhost

granularity:1

extrafine:1

I would like to know if there exist an easy way to fix it, because I would like 
to avoid any important modification in my security pc's stuff.

Is it a new modification? or a strictly problem of the user (me!)

Thanks in advance

Ricardo

p.s.: this is my OPTION file

current:FOPT:-FR -O3 -mp1 -w -prec_div -pc80 -pad -align -DINTEL_VML

current:FPOPT:$(FOPT)

current:LDFLAGS:$(FOPT) -L/opt/intel/Compiler/11.0/081/mkl/lib/em64t -pthread 
-i-static

current:DPARALLEL:'-DParallel'

current:R_LIBS:-lmkl_lapack -lmkl -lguide -lmkl_scalapack -lmkl_blacs_lp64

current:RP_LIBS:-lmkl_intel_lp64 -lmkl_scalapack_lp64 -lmkl_blacs_lp64 
-lmkl_sequential -L /opt/local/fftw/lib/ -lfftw_mpi -lfftw

current:MPIRUN:

-
  Dr. Ricardo Faccio
  Prof. Adjunto de F?sica 
  Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA
  Facultad de Qu?mica, Universidad de la Rep?blica
   Av. Gral. Flores 2124, C.C. 1157
   C.P. 11800, Montevideo, Uruguay.
  E-mail: rfaccio at fq.edu.uy
  Phone: 598 2 924 98 59
  598 2 929 06 48
  Fax:598 2 9241906
  Web:  http://cryssmat.fq.edu.uy/ricardo/ricardo.htm
-
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[Wien] parallel calculation stops waiting for a pass in ssh root@localhost

[Duy Le]

You should check the permission of .ssh and files therein. For
instance:drwx--
.ssh
-rw-r--r--   id_rsa.pub
-rw---   id_rsa
-rw-r--r--   authorized_keys
-rw-r--r--   known_hosts

If it still doesn't work, open  authorized_keys file and delete lines
related to your host.
Then use ssh-keygen to generate new key without password, then cat
id_rsa.pub  authorized_keys.

Good luck.


2009/10/1 Ricardo Faccio rfaccio at fq.edu.uy

  Dear Wien users

 I have some problems in using parallelization over kpoints in the latest
 release of WIEN2k. It is important to mention that I had no troubles in the
 past with my settings.

 In particular I am working with dual-core pc desktops, and one Quad-core
 machines, individually. For instance, in a simple parallel setup, the
 typical test_case, I found this:

 -

 root at rfaccio:/home/rfaccio/calculo/wien2k/test_case# x lapw1 -c -up -p

 starting parallel lapw1 at Thu Oct  1 23:32:56 UYT 2009

 -  starting parallel LAPW1 jobs at Thu Oct  1 23:32:56 UYT 2009

 running LAPW1 in parallel mode (using .machines)

 2 number_of_parallel_jobs

 [1] 30629

 root at localhost's password:

 -

 As you can see the code keeps waiting for my password. It never happened
 before, and it seems to have no relationship with the shared memory setup
 because I used the same flags than in previous release versions.

 I use this .machine file:

 1:localhost

 1:localhost

 granularity:1

 extrafine:1

 I would like to know if there exist an easy way to fix it, because I would
 like to avoid any important modification in my security pc's stuff.

 Is it a new modification? or a strictly problem of the user (me!)

 Thanks in advance

 Ricardo

 p.s.: this is my OPTION file

 current:FOPT:-FR -O3 -mp1 -w -prec_div -pc80 -pad -align -DINTEL_VML

 current:FPOPT:$(FOPT)

 current:LDFLAGS:$(FOPT) -L/opt/intel/Compiler/11.0/081/mkl/lib/em64t
 -pthread -i-static

 current:DPARALLEL:'-DParallel'

 current:R_LIBS:-lmkl_lapack -lmkl -lguide -lmkl_scalapack -lmkl_blacs_lp64

 current:RP_LIBS:-lmkl_intel_lp64 -lmkl_scalapack_lp64 -lmkl_blacs_lp64
 -lmkl_sequential -L /opt/local/fftw/lib/ -lfftw_mpi -lfftw

 current:MPIRUN:
 -
   Dr. Ricardo Faccio
   Prof. Adjunto de F?sica
   Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA
   Facultad de Qu?mica, Universidad de la Rep?blica
Av. Gral. Flores 2124, C.C. 1157
C.P. 11800, Montevideo, Uruguay.
   E-mail: rfaccio at fq.edu.uy
   Phone: 598 2 924 98 59
   598 2 929 06 48
   Fax:598 2 9241906
   Web:  http://cryssmat.fq.edu.uy/ricardo/ricardo.htm

 -

 ___
 Wien mailing list
 Wien at zeus.theochem.tuwien.ac.at
 http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien




-- 
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.
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[Wien] parallel calculation stops waiting for a pass in ssh root@localhost

[Peter Blaha]

First about security:   You should NOT run ieN2k as user root.

root is the system administrator, and one should be root ONLY when doing 
sysadmin tasks.
Create a regular user and run normal work as restricted user.

k-parallelization has 2 options during siteconfig:

shared memory machine: This does NOT use ssh to span the parallel 
jobs, but simply starts eg. 4 lapw1 jobs (in background) on the local 
machine. This is the most simple option when you have eg. a single 
quadcore PC, but you cannot parallelize between 2 different PCs.

no shared memory: It will use a command like
ssh pcX  lapw0 lapw0.def ...
to start a job on a remote but also on the local computer.

Thus you need to be able to do passwordless ssh  to your local computer.

Try   ssh localhostand you must be able to login WITHOUT typing a 
password. For setup of this you must use ssh-keygen, for details see eg. 
the UG.


Ricardo Faccio schrieb:
 Dear Wien users
 
 I have some problems in using parallelization over kpoints in the latest 
 release of WIEN2k. It is important to mention that I had no troubles in 
 the past with my settings.
 
 In particular I am working with dual-core pc desktops, and one Quad-core 
 machines, individually. For instance, in a simple parallel setup, the 
 typical test_case, I found this:
 
 -
 
 root at rfaccio:/home/rfaccio/calculo/wien2k/test_case# x lapw1 -c -up -p
 
 starting parallel lapw1 at Thu Oct  1 23:32:56 UYT 2009
 
 -  starting parallel LAPW1 jobs at Thu Oct  1 23:32:56 UYT 2009
 
 running LAPW1 in parallel mode (using .machines)
 
 2 number_of_parallel_jobs
 
 [1] 30629
 
 root at localhost's password:
 
 -
 
 As you can see the code keeps waiting for my password. It never happened 
 before, and it seems to have no relationship with the shared memory 
 setup because I used the same flags than in previous release versions.
 
 I use this .machine file:
 
 1:localhost
 
 1:localhost
 
 granularity:1
 
 extrafine:1
 
 I would like to know if there exist an easy way to fix it, because I 
 would like to avoid any important modification in my security pc's stuff.
 
 Is it a new modification? or a strictly problem of the user (me!)
 
 Thanks in advance
 
 Ricardo
 
 p.s.: this is my OPTION file
 
 current:FOPT:-FR -O3 -mp1 -w -prec_div -pc80 -pad -align -DINTEL_VML
 
 current:FPOPT:$(FOPT)
 
 current:LDFLAGS:$(FOPT) -L/opt/intel/Compiler/11.0/081/mkl/lib/em64t 
 -pthread -i-static
 
 current:DPARALLEL:'-DParallel'
 
 current:R_LIBS:-lmkl_lapack -lmkl -lguide -lmkl_scalapack -lmkl_blacs_lp64
 
 current:RP_LIBS:-lmkl_intel_lp64 -lmkl_scalapack_lp64 -lmkl_blacs_lp64 
 -lmkl_sequential -L /opt/local/fftw/lib/ -lfftw_mpi -lfftw
 
 current:MPIRUN:
 
 -
   Dr. Ricardo Faccio
   Prof. Adjunto de F?sica
   Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA
   Facultad de Qu?mica, Universidad de la Rep?blica
Av. Gral. Flores 2124, C.C. 1157
C.P. 11800, Montevideo, Uruguay.
   E-mail: rfaccio at fq.edu.uy mailto:rfaccio at fq.edu.uy
   Phone: 598 2 924 98 59
   598 2 929 06 48
   Fax:598 2 9241906
   Web:  http://cryssmat.fq.edu.uy/ricardo/ricardo.htm
 -
 
 
 
 
 ___
 Wien mailing list
 Wien at zeus.theochem.tuwien.ac.at
 http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien

-- 
-
Peter Blaha
Inst. Materials Chemistry, TU Vienna
Getreidemarkt 9, A-1060 Vienna, Austria
Tel: +43-1-5880115671
Fax: +43-1-5880115698
email: pblaha at theochem.tuwien.ac.at
-

[Wien] parallel calculation stops waiting for a pass inssh root@localhost

[Ricardo Faccio]

Dear Prof. Blaha  and Duy Le

Thanks for your help, but I found modifying lapw1cpara and lapw1para 
scripts by hand, they can work properly for me.

#

#In this section use 0 to turn of an option, 1 to turn it on,

#respectively choose a value



set useremote   = 0 # using remote shell to launch processes

set mpiremote   = 1 # using remote shell to launch mpi

set delay   = 1 # delay launching of processes by n seconds

set sleepy  = 1 # additional sleep before checking

set debug   = 0 # verbosity of debugging output



#

Thanks once again

Ricardo

-
  Dr. Ricardo Faccio
  Prof. Adjunto de F?sica
  Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA
  Facultad de Qu?mica, Universidad de la Rep?blica
   Av. Gral. Flores 2124, C.C. 1157
   C.P. 11800, Montevideo, Uruguay.
  E-mail: rfaccio at fq.edu.uy
  Phone: 598 2 924 98 59
  598 2 929 06 48
  Fax:598 2 9241906
  Web:  http://cryssmat.fq.edu.uy/ricardo/ricardo.htm
-
- Original Message - 
From: Peter Blaha pbl...@theochem.tuwien.ac.at
To: A Mailing list for WIEN2k users wien at zeus.theochem.tuwien.ac.at
Sent: Friday, October 02, 2009 3:40 AM
Subject: Re: [Wien] parallel calculation stops waiting for a pass inssh 
root at localhost


 First about security:   You should NOT run ieN2k as user root.

 root is the system administrator, and one should be root ONLY when doing 
 sysadmin tasks.
 Create a regular user and run normal work as restricted user.

 k-parallelization has 2 options during siteconfig:

 shared memory machine: This does NOT use ssh to span the parallel jobs, 
 but simply starts eg. 4 lapw1 jobs (in background) on the local machine. 
 This is the most simple option when you have eg. a single quadcore PC, but 
 you cannot parallelize between 2 different PCs.

 no shared memory: It will use a command like
 ssh pcX  lapw0 lapw0.def ...
 to start a job on a remote but also on the local computer.

 Thus you need to be able to do passwordless ssh  to your local computer.

 Try   ssh localhostand you must be able to login WITHOUT typing a 
 password. For setup of this you must use ssh-keygen, for details see eg. 
 the UG.


 Ricardo Faccio schrieb:
 Dear Wien users

 I have some problems in using parallelization over kpoints in the latest 
 release of WIEN2k. It is important to mention that I had no troubles in 
 the past with my settings.

 In particular I am working with dual-core pc desktops, and one Quad-core 
 machines, individually. For instance, in a simple parallel setup, the 
 typical test_case, I found this:

 -

 root at rfaccio:/home/rfaccio/calculo/wien2k/test_case# x lapw1 -c -up -p

 starting parallel lapw1 at Thu Oct  1 23:32:56 UYT 2009

 -  starting parallel LAPW1 jobs at Thu Oct  1 23:32:56 UYT 2009

 running LAPW1 in parallel mode (using .machines)

 2 number_of_parallel_jobs

 [1] 30629

 root at localhost's password:

 -

 As you can see the code keeps waiting for my password. It never happened 
 before, and it seems to have no relationship with the shared memory setup 
 because I used the same flags than in previous release versions.

 I use this .machine file:

 1:localhost

 1:localhost

 granularity:1

 extrafine:1

 I would like to know if there exist an easy way to fix it, because I 
 would like to avoid any important modification in my security pc's stuff.

 Is it a new modification? or a strictly problem of the user (me!)

 Thanks in advance

 Ricardo

 p.s.: this is my OPTION file

 current:FOPT:-FR -O3 -mp1 -w -prec_div -pc80 -pad -align -DINTEL_VML

 current:FPOPT:$(FOPT)

 current:LDFLAGS:$(FOPT) -L/opt/intel/Compiler/11.0/081/mkl/lib/em64t 
 -pthread 
  -i-static

 current:DPARALLEL:'-DParallel'

 current:R_LIBS:-lmkl_lapack -lmkl -lguide -lmkl_scalapack -lmkl_blacs_lp64

 current:RP_LIBS:-lmkl_intel_lp64 -lmkl_scalapack_lp64 -lmkl_blacs_lp64 
 -lmkl_sequential 
  -L /opt/local/fftw/lib/ -lfftw_mpi -lfftw

 current:MPIRUN:

 -
   Dr. Ricardo Faccio
   Prof. Adjunto de F?sica
   Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA
   Facultad de Qu?mica, Universidad de la Rep?blica
Av. Gral. Flores 2124, C.C. 1157
C.P. 11800, Montevideo, Uruguay.
   E-mail: rfaccio at fq.edu.uy mailto:rfaccio at fq.edu.uy
   Phone: 598 2 924 98 59
   598 2 929 06 48
   Fax:598 2 9241906
   Web:  http://cryssmat.fq.edu.uy/ricardo/ricardo.htm