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

Laurence Marks L-marks at northwestern.edu
Mon Nov 2 16:01:41 CET 2015 

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=320000
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 <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.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
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