[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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