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

Peter Blaha pblaha at theochem.tuwien.ac.at
Wed Nov 4 17:21:07 CET 2015


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)
10000**2*10=10**9 bytes = 1GB
NMATMAX=20000: ~4GB (per core !!)

c) larger values than 20000 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=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 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
> <mailto: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 <http://www.numis.northwestern.edu>
> Corrosion in 4D: MURI4D.numis.northwestern.edu
> <http://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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-- 

                                       P.Blaha
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Email: blaha at theochem.tuwien.ac.at    WIEN2k: http://www.wien2k.at
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