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

Wed Nov 4 15:04:42 CET 2015

Thanks.For the NMATMAX and NUME values, I am following the prompt during installation:"NMATMAX=10000 ==>   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 set    NUME=NMATMAX/10."I have 128GB at node1 and 64GB memory at node2 . So, I assume that 32GB should be available for WIEN2k. Then 32*10000=320000, 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-marks at northwestern.edu
To: wien at 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 valuesset value for NMATMAX=320000set 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 <weitongwei at 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"

                  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/xxxxx (xxxx=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 statement,No Makefile.orig****** )

    .....

    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. 
   **********************************

   *  Configure parallel execution  *

   **********************************  

  Shared Memory Architecture? (y/N):N

  If you are using mpi2 set MPI_REMOTE to 0

  Set MPI_REMOTE to  0 / 1: 1
   **********************************

   *  Configure parallel execution  *

   **********************************

     Remote shell (default is ssh) = ssh

 ********************************************************

     You need to KNOW details about your installed  MPI and FFTW )
   (y/n) y

      Your compiler: mpif90

 Finding the required fftw2/3 mpi-files in /usr and /opt ....

/usr/local/fftw3.3.4/lib/libfftw3_mpi.a

could not find fftw ....           (*************here I don't know why not found**********)

Your present FFTW choice is:   

Please specify whether you want to use FFTW3 (default) or FFTW2  (FFTW3 / FFTW2): FFTW3
Present FFTWpath is:  

Please specify the ROOT-path of your FFTW installation (like /opt/fftw3): /usr/local/fftw3.3.4

Your FFTW_LIBS are: -lfftw3_mpi -lfftw3 -L/usr/local/fftw3.3.4/lib 

Your FFTW_OPT are : -DFFTW3 -I/usr/local/fftw3.3.4/include 

is this correct? enter Y (default) or n: Y
The blacs-library depends on the version of your mpi (intelmpi, openmpi,

sgimpi, others) and you have to specify the proper blacs-library

in /opt/intel/composer_xe_2013.5.192/mkl/lib/intel64 you have the following blacs libraries:

/opt/intel/composer_xe_2013.5.192/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a

/opt/intel/composer_xe_2013.5.192/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so

/opt/intel/composer_xe_2013.5.192/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.a

/opt/intel/composer_xe_2013.5.192/mkl/lib/intel64/libmkl_blacs_sgimpt_lp64.a

   Current settings:
     FFTW_LIB + FFTW_OPT    : -lfftw3_mpi -lfftw3 -L/usr/local/fftw3.3.4/lib  +  -DFFTW3 -I/usr/local/fftw3.3.4/include (already set)

     RP  RP_LIB(SCALAPACK+PBLAS): -lmkl_scalapack_lp64 -lmkl_blacs_lp64 $(R_LIBS)

     FP  FPOPT(par.comp.options): $(FOPT)

     MP  MPIRUN commando        : mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_

   *******************************

   *  Changing compiler options  *

   *******************************

    changing Makefile in SRC_lapw0

    changing Makefile in SRC_lapw1

    changing Makefile in SRC_lapw2

    changing Makefile in SRC_hf

    changing Makefile in SRC_dstart

    changing Makefile in SRC_lapwso

    changing Makefile in SRC_nmr
   ***********************************

   *    (Re-)Dimension parameters    *

   ***********************************

set value for NMATMAX=320000

set value for NUME=32000
   ************************************

   *    Compile/Recompile programs    *

   ************************************
      A   Compile all programs (suggested)
      Selection: A

**********I watched the screen and saw a few errors in the following*****************

RC_BerryPI ...

make: *** No rule to make target `clean'.  Stop.

make: *** No targets specified and no makefile found.  Stop.
SRC_clmcopy ...

rm  -f clmcopy.o modules.o  reallocate.o struct_afm_check.o readstruct.o writestruct.o outerr.o  *.mod

ifort  -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -O3 -xW   -c clmcopy.f

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

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

make: Circular reallocate.o <- reallocate.o dependency dropped.
ifort: command line remark #10010: option '-pthread' is deprecated and will be removed in a future release. See '-help deprecated'

make[1]: Leaving directory `/usr/local/WIEN2k_14.2/SRC_dstart'

make: *** No rule to make target `complex'.  Stop.
......

Copying programs

  SRC_afminput/afminput

  ......

  SRC_BerryPI/BerryPI

cp: omitting directory `SRC_BerryPI/BerryPI'

  SRC_broadening/broadening

  .....

  SRC_w2w/w2w

  SRC_w2w/w2wc

  SRC_w2web/w2web

cp: `SRC_w2web/w2web' and `/usr/local/WIEN2k_14.2/w2web' are the same file

  SRC_wplot/wplot

  SRC_wplot/wplotc

  SRC_structeditor/SRC_ncmsymmetry/ncmsymmetry

  SRC_structeditor/SRC_readwrite/readwrite

  SRC_structeditor/SRC_struct2mol/struct2mol

  SRC_structeditor/SRC_structgen/structgen
done.

-- 
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.eduCorrosion 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

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