Re: [Wien] Some error messages during Installation of WIEN2k_14.2 on CentOS6.5

[Laurence Marks]

What you wrote is right...and wrong.

If you are just running 1 process at a time in the non-parallel mode, what
you wrote is correct.

However, in many cases one either runs  many different processes
simultaneously, often as many as you have cores (ignoring hyperthreading
which is rarely useful in my experience). For larger calculations you may
also want to use mpi in which case every core will have the same memory
usage.

You have a relatively small cluster, so I suggest that you leave it with
the default values, particularly if you are relatively new to Wien2k. While
the values you used probably won't matter, they are not that safe. I
suggest leaving them for now and running a number of test calculations.

On Wed, Nov 4, 2015 at 8:04 AM, tongwei <weitong...@hotmail.com> wrote:

> Thanks.
> For the NMATMAX and NUME values, I am following the prompt during
> installation:
> "NMATMAX=1 ==>   1GB (real) (==> cells with about 50-150
> atoms/unitcell)
> ==> for lapw1c:NMATMAX will be reduced internally to NMATMAX/sqrt2
> ==> for lapw1_mpi: NMATMAX will be increased internally to
> NMATMAX*sqrt(NP)
>
> NUME determines the number of states to output. As a rule of thumb one can
> estimate 100 basis functions per atom in the cell and 10 occupied states
> per
> atom, so setNUME=NMATMAX/10.
> "
> I have 128GB at node1 and 64GB memory at node2 . So, I assume that 32GB
> should be available for WIEN2k. Then 32*1=32, NUME=NMATMAX/10=32000.
>
> Is this wrong? Then, where to change this value?
>
> Best,
> WT
>
> --
> Date: Mon, 2 Nov 2015 09:01:41 -0600
> From: l-ma...@northwestern.edu
> To: wien@zeus.theochem.tuwien.ac.at
> Subject: Re: [Wien] Some error messages during Installation of WIEN2k_14.2
> on CentOS6.5
>
> I am 99.9% certain that none of these is an error. The compile script will
> tell you if there are any at the end, these are flagged with "Error".
>
> N.B., the values
> set value for NMATMAX=32
> set value for NUME=32000
>
> are large, you could run into problems with these if you are running
> k-point parallel for larger jobs. Since you only have a 2 node cluster with
> 1G ethernet (?) you may be only intending to run smaller jobs in which case
> it will be fine. You could get an OOM (Out Of Memory) OS crash with larger
> jobs.
>
>
> --
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu
Corrosion in 4D: MURI4D.numis.northwestern.edu
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] Some error messages during Installation of WIEN2k_14.2 on CentOS6.5

[Peter Blaha]

Yes it is wrong.

a) The memory count usually as memory/core, so if you have a 64GB node, 
you should most likely divide by the number of cores (and then maybe 
multiply by 2, because you can use multithreading with 2 cores and use 2 
cores/job.
b) The memory is calculated as:  NMATMAX**2 * 10 (actually it should be 
8 bytes/number, but we need also some overhead)

1**2*10=10**9 bytes = 1GB
NMATMAX=2: ~4GB (per core !!)

c) larger values than 2 are most likely useless, because as was said 
by L.Marks, for larger cases there is no k-parallism but even when it 
would fit in memory, it would run much too long. Therefore we switch to 
mpi-parallelization with many cores (on a good cluster AND big problem 
we have used up to 1000 cores).
And for these problems NMTMAX will be internally increased by 
NMATMAX*sqrt(NP)


On 11/04/2015 03:04 PM, tongwei wrote:

Thanks.
For the NMATMAX and NUME values, I am following the prompt during
installation:
"NMATMAX=1 ==>   1GB (real) (==> cells with about 50-150 atoms/unitcell)
 ==> for lapw1c:NMATMAX will be reduced internally to NMATMAX/sqrt2
 ==> for lapw1_mpi: NMATMAX will be increased internally to
NMATMAX*sqrt(NP)

NUME determines the number of states to output. As a rule of thumb one can
estimate 100 basis functions per atom in the cell and 10 occupied states
per
atom, so setNUME=NMATMAX/10.
"
I have 128GB at node1 and 64GB memory at node2 . So, I assume that 32GB
should be available for WIEN2k. Then 32*1=32,
NUME=NMATMAX/10=32000.
Is this wrong? Then, where to change this value?

Best,
WT


Date: Mon, 2 Nov 2015 09:01:41 -0600
From: l-ma...@northwestern.edu
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] Some error messages during Installation of
WIEN2k_14.2 on CentOS6.5

I am 99.9% certain that none of these is an error. The compile script
will tell you if there are any at the end, these are flagged with "Error".

N.B., the values
set value for NMATMAX=32
set value for NUME=32000

are large, you could run into problems with these if you are running
k-point parallel for larger jobs. Since you only have a 2 node cluster
with 1G ethernet (?) you may be only intending to run smaller jobs in
which case it will be fine. You could get an OOM (Out Of Memory) OS
crash with larger jobs.

On Mon, Nov 2, 2015 at 8:51 AM, tongwei <weitong...@hotmail.com
<mailto:weitong...@hotmail.com>> wrote:

Dear Everyone,

During installing WIEN2k_14.2, I watched the screen and saw a few
errors in the following.  I am not sure it is OK or not.
---after save compiler options---
No Makefile.orig in SRC_structeditor/SRC_lib, leaving directory.
No Makefile.orig in SRC_BerryPI, leaving directory.
No Makefile.orig in SRC_lib, leaving directory.
No Makefile.orig in SRC_structeditor, leaving directory.
No Makefile.orig in SRC_templates, leaving directory.
  No Makefile.orig in SRC_usersguide_html, leaving directory.
No Makefile.orig in SRC_w2web, leaving directory.
-During compiling-
RC_BerryPI ...
make: *** No rule to make target `clean'.  Stop.
make: *** No targets specified and no makefile found.  Stop.

SRC_clmcopy ...
make: Circular modules.o <- modules.o dependency dropped.
make: Circular reallocate.o <- modules.o dependency dropped.
make: Circular reallocate.o <- reallocate.o dependency dropped.

make[1]: Leaving directory `/usr/local/WIEN2k_14.2/SRC_dstart'
make: *** No rule to make target `complex'.  Stop.
---

Waiting for solution.
Thanks!

WT

+++Here is my situation and installation process

1. Hardware: A simple cluster with TWO DELL T760/T7600 workstations
communicating through 1000M switch:
Master (node1)--- 2*Xeon E5-2690 (2*8core), 128G memory
Slave (node2)  2*Xeon E5-2690 v2 (2*10core), 64G memory
---Installation is on Master.
2. OS: CentOS 6.5 64bit final
3. Required package installed
F90 compiler Intel parallel_studio_xe_2013_update4 inluding
ifort version 13.1.3, icc version 13.1.3, MKL, installed at /opt/intel
perl 5   v5.10.1 installed at  /usr/bin/perl)
emacs --- GNU Emacs 23.1.1 installed at /usr/bin/emacs）
ghostscript  v8.70 installed at /usr/bin/ghostscript)
gnuplot - gnuplot 4.2 patchlevel 6 installed at /usr/bin/gnuplot ）
www-browser - firefox 38.2.1 installed
Tcl/Tk-Toolkit - tcl.x86_64/tk.x86_64 v8.5.7 installed
FFTW v.2 or 3 -Both installed with yum (fftw2-2.1.5, fftw-3.2.1),
   and also installed fftw3.3.4 from source through
   "./configure --prefix=/usr/local/fftw3.3.4
CC="icc" --enable-mpi --enable-threads"
  

Re: [Wien] Some error messages during Installation of WIEN2k_14.2 on CentOS6.5

[Laurence Marks]

I am 99.9% certain that none of these is an error. The compile script will
tell you if there are any at the end, these are flagged with "Error".

N.B., the values
set value for NMATMAX=32
set value for NUME=32000

are large, you could run into problems with these if you are running
k-point parallel for larger jobs. Since you only have a 2 node cluster with
1G ethernet (?) you may be only intending to run smaller jobs in which case
it will be fine. You could get an OOM (Out Of Memory) OS crash with larger
jobs.

On Mon, Nov 2, 2015 at 8:51 AM, tongwei  wrote:

> Dear Everyone,
>
> During installing WIEN2k_14.2, I watched the screen and saw a few errors
> in the following.  I am not sure it is OK or not.
> ---after save compiler options---
> No Makefile.orig in SRC_structeditor/SRC_lib, leaving directory.
> No Makefile.orig in SRC_BerryPI, leaving directory.
> No Makefile.orig in SRC_lib, leaving directory.
> No Makefile.orig in SRC_structeditor, leaving directory.
> No Makefile.orig in SRC_templates, leaving directory.
>  No Makefile.orig in SRC_usersguide_html, leaving directory.
> No Makefile.orig in SRC_w2web, leaving directory.
> -During compiling-
> RC_BerryPI ...
> make: *** No rule to make target `clean'.  Stop.
> make: *** No targets specified and no makefile found.  Stop.
>
> SRC_clmcopy ...
> make: Circular modules.o <- modules.o dependency dropped.
> make: Circular reallocate.o <- modules.o dependency dropped.
> make: Circular reallocate.o <- reallocate.o dependency dropped.
>
> make[1]: Leaving directory `/usr/local/WIEN2k_14.2/SRC_dstart'
> make: *** No rule to make target `complex'.  Stop.
> ---
>
> Waiting for solution.
> Thanks!
>
> WT
>
> +++Here is my situation and installation process
>
> 1. Hardware: A simple cluster with TWO DELL T760/T7600 workstations
> communicating through 1000M switch:
> Master (node1)--- 2*Xeon E5-2690 (2*8core), 128G memory
> Slave (node2)  2*Xeon E5-2690 v2 (2*10core), 64G memory
> ---Installation is on Master.
> 2. OS: CentOS 6.5 64bit final
> 3. Required package installed
> F90 compiler Intel parallel_studio_xe_2013_update4 inluding ifort
> version 13.1.3, icc version 13.1.3, MKL, installed at /opt/intel
> perl 5   v5.10.1 installed at  /usr/bin/perl)
> emacs --- GNU Emacs 23.1.1 installed at /usr/bin/emacs）
> ghostscript  v8.70 installed at /usr/bin/ghostscript)
> gnuplot - gnuplot 4.2 patchlevel 6 installed at /usr/bin/gnuplot ）
> www-browser - firefox 38.2.1 installed
> Tcl/Tk-Toolkit - tcl.x86_64/tk.x86_64 v8.5.7 installed
> FFTW v.2 or 3 -Both installed with yum (fftw2-2.1.5, fftw-3.2.1),
>   and also installed fftw3.3.4 from source through
>   "./configure --prefix=/usr/local/fftw3.3.4 CC="icc"
> --enable-mpi --enable-threads"
>   and "make", "make install" at /usr/local/fftw3.3.4 with
> parallel available.
> MPI+SCALAPACK -Yum installed mpich-3.1-4, openmpi-1.8.1,
> scalapack-common-2.0.2,
> scalapack-openmpi-2.0.2,scalapack-mpich-2.0.2,blacs-common-2.0.2,blacs-mpich-2.0.2,
> blacs-openmpi-2.0.2
>Also mpich-3.1 was installed from source  at
> /usr/local/mpich3_intel13 (compiled with ifort13 and icc13
> compiler)This mpich path is indicated in the bashrc and profile*
> Python  Python 2.6.6 (with numpy1.4) came with OS,
> Python 2.7.3 installed at /usr/local/lib/python2.7,
> /usr/local/bin
> New Numpy 1.8.0 was uninstalled, and Numpy 1.6.2 was installed
> with Python 2.7.3.
> Intel MKL-fft Intel MKL-fft was compiled through "make libintel64
> F=intel precision=MKL_DOUBLE" at /opt/intel/mkl/interfaces/x
> (=fftw2xc  fftw2xf  fftw3xc fftw3xf)
> 4. Install WIEN2k_14.2
> mkdir "WIEN2k_14.2" at /usr/local/
> copy Fccni.tar.gz  TiC.tar.gz  TiO2.tar.gz  WIEN2k_14.2.tar to
> /usr/local/WIEN2k_14.2, then:
> # tar -xvf WIEN2k_14.2.tar
> # gunzip *.gz
> # chmod +x ./expand_lapw
> # ./expand_lapw
> ***Everything is unpacked except Fccni.tar*, then
> # tar -xf Fccni.tar
> # ./siteconfig_lapw
>**
>*  Specify a system  *
>**
>  Selection: I
>
>***
>*  Specify compilers  *
>***
> Your Fortran compiler will be ifort.
> Your C compiler will be cc.
>**
>*  Specify compiler options  *
>**
> searching 
> You have the following mkl libraries in
> /opt/intel/composer_xe_2013.5.192/mkl/lib/intel64 :
>
> /opt/intel/composer_xe_2013.5.192/mkl/lib/intel64/libmkl_blacs_intelmpi_ilp64.so
> ..
> /opt/intel/composer_xe_2013.5.192/mkl/lib/intel64/libmkl_lapack95_ilp64.a
> MKL_TARGET_ARCH was set to intel64
> The default options shown on the next screen should be ok
> Hit Enter to continue
> Current settings:
>  O   Compiler 

[Wien] Some error messages during Installation of WIEN2k_14.2 on CentOS6.5

[tongwei]

Dear Everyone,

During installing WIEN2k_14.2, I watched the screen and saw a few errors in the 
following.  I am not sure it is OK or not.
---after save compiler options---
No Makefile.orig in SRC_structeditor/SRC_lib, leaving directory.
No Makefile.orig in SRC_BerryPI, leaving directory. 
No Makefile.orig in SRC_lib, leaving directory. 
No Makefile.orig in SRC_structeditor, leaving directory.
No Makefile.orig in SRC_templates, leaving directory.
 No Makefile.orig in SRC_usersguide_html, leaving directory.
No Makefile.orig in SRC_w2web, leaving directory.
-During compiling-
RC_BerryPI ...
make: *** No rule to make target `clean'.  Stop.
make: *** No targets specified and no makefile found.  Stop.

SRC_clmcopy ...
make: Circular modules.o <- modules.o dependency dropped.
make: Circular reallocate.o <- modules.o dependency dropped.
make: Circular reallocate.o <- reallocate.o dependency dropped.

make[1]: Leaving directory `/usr/local/WIEN2k_14.2/SRC_dstart'
make: *** No rule to make target `complex'.  Stop.
---

Waiting for solution.
Thanks!

WT

+++Here is my situation and installation process

1. Hardware: A simple cluster with TWO DELL T760/T7600 workstations 
communicating through 1000M switch: 
Master (node1)--- 2*Xeon E5-2690 (2*8core), 128G memory
Slave (node2)  2*Xeon E5-2690 v2 (2*10core), 64G memory
---Installation is on Master.
2. OS: CentOS 6.5 64bit final3. Required package installed 
F90 compiler Intel parallel_studio_xe_2013_update4 inluding ifort version 
13.1.3, icc version 13.1.3, MKL, installed at /opt/intel
perl 5   v5.10.1 installed at  /usr/bin/perl)
emacs --- GNU Emacs 23.1.1 installed at /usr/bin/emacs）
ghostscript  v8.70 installed at /usr/bin/ghostscript) 
gnuplot - gnuplot 4.2 patchlevel 6 installed at /usr/bin/gnuplot ）
www-browser - firefox 38.2.1 installed
Tcl/Tk-Toolkit - tcl.x86_64/tk.x86_64 v8.5.7 installed
FFTW v.2 or 3 -Both installed with yum (fftw2-2.1.5, fftw-3.2.1), 
  and also installed fftw3.3.4 from source through 
  "./configure --prefix=/usr/local/fftw3.3.4 CC="icc" 
--enable-mpi --enable-threads"
  and "make", "make install" at /usr/local/fftw3.3.4 with 
parallel available.
MPI+SCALAPACK -Yum installed mpich-3.1-4, openmpi-1.8.1, 
scalapack-common-2.0.2, 
scalapack-openmpi-2.0.2,scalapack-mpich-2.0.2,blacs-common-2.0.2,blacs-mpich-2.0.2,
 blacs-openmpi-2.0.2
   Also mpich-3.1 was installed from source  at 
/usr/local/mpich3_intel13 (compiled with ifort13 and icc13 compiler)This 
mpich path is indicated in the bashrc and profile*Python  Python 2.6.6 
(with numpy1.4) came with OS, 
Python 2.7.3 installed at /usr/local/lib/python2.7, /usr/local/bin
New Numpy 1.8.0 was uninstalled, and Numpy 1.6.2 was installed with 
Python 2.7.3.Intel MKL-fft Intel MKL-fft was compiled through "make 
libintel64 F=intel precision=MKL_DOUBLE" at /opt/intel/mkl/interfaces/x 
(=fftw2xc  fftw2xf  fftw3xc fftw3xf)4. Install WIEN2k_14.2  
mkdir "WIEN2k_14.2" at /usr/local/
copy Fccni.tar.gz  TiC.tar.gz  TiO2.tar.gz  WIEN2k_14.2.tar to 
/usr/local/WIEN2k_14.2, then:# tar -xvf WIEN2k_14.2.tar 
# gunzip *.gz
# chmod +x ./expand_lapw
# ./expand_lapw ***Everything is unpacked except Fccni.tar*, then
# tar -xf Fccni.tar# ./siteconfig_lapw   **
   *  Specify a system  *
   **
 Selection: I
 
   ***
   *  Specify compilers  *
   ***
Your Fortran compiler will be ifort.
Your C compiler will be cc.   **
   *  Specify compiler options  *
   **
searching 
You have the following mkl libraries in 
/opt/intel/composer_xe_2013.5.192/mkl/lib/intel64 :
/opt/intel/composer_xe_2013.5.192/mkl/lib/intel64/libmkl_blacs_intelmpi_ilp64.so
..
/opt/intel/composer_xe_2013.5.192/mkl/lib/intel64/libmkl_lapack95_ilp64.a
MKL_TARGET_ARCH was set to intel64
The default options shown on the next screen should be ok
Hit Enter to continue Current settings:
 O   Compiler options:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML 
-O3 -xW
 F   FFTW options:
 L   Linker Flags:$(FOPT) 
-L/opt/intel/composer_xe_2013.5.192/mkl/lib/intel64/ -pthread -i-static
 P   Preprocessor flags   '-DParallel'
 R   R_LIB (LAPACK+BLAS): -lmkl_lapack95_lp64 -lmkl_intel_lp64 
-lmkl_intel_thread -lmkl_core -openmp -lpthread
 FL  FFTW_LIBS:   -lfftw3_mpi -lfftw3 
-L/usr/local/fftw3_intel12_mpich3/lib
 S   Save and Quit  ***
   *  Changing compiler options  *
   ***changing Makefile in SRC_lib/blas_lapw
changing Makefile in SRC_lib/lapack_lapw
No Makefile.orig in SRC_structeditor/SRC_lib, leaving directory.  
(*There are several this