No subject
Wed Sep 23 10:56:00 CEST 2009
k-point parallelization in my system, even though I tried to modify
.machines file for my system (modified files are attached below).
Are there any other parameters (e.g., emax, RMT radii, etc.) that I should
change upon the calculation to get the correct results with large size super
cell? (I could not find any related comments about dependence of calculation
parameters on lattice parameter or number of atoms.)
As for the calculation time, I just wonder whether this could be due to some
problems associated with compilation options for my system (see below for
the details).
(5) Other questions (about RAM usage during lapw* calculation)
I set the NMATMAX and NUME parameters as suggested by the Wien2K manual; I
calculated these values for a memory size of 24G.
# NMATMAX = sqrt( RAM/10), RAM is the size of memory in byte.
# NUME = NMATMAX/10
However, when I type 'top -c' in the terminal, the RAM usage for each single
program, (e.g. lapw1 and lapw2..) is only about 2~3 %. I think this is very
low, and thus wonder whether it functions properly or not. However, when I
use 'free' commend, the usage of memory is almost full. Please let me know
how this program controls the memory usage of each single program.
_____
(a) System specification
CPU: dual CPU (intel xeon quad core X5550)
RAM: 24G
OS: RHE 5.3
Compiler: ifort 11
MKL: intel 10.4
(b) Modified .machines file
1:localhost (total 8 lines of local host, because the total thread is 8)
.
1:localhost
granularity:1
xxtrafine:1
Are there any things what I have to attach this file? The problems of
parallelization may be come from the misses of this file; and I just want to
know that is it possible to use parallelization on my system (SMP) without
installing MPI library?
(c) The compilation options (copied from OPTIONS file)
current:FOPT:-FR -mp1 -w -prec_div -pc80 -pad -align -DINTEL_VML -O3
-xSSE4.1
current:FPOPT:$(FOPT)
current:LDFLAGS:$(FOPT) -L/opt/intel/mkl/10.2.1.017/lib/em64t -pthread
current:DPARALLEL:'-DParallel'
current:R_LIBS:-L/opt/intel/mkl/10.2.1.017/lib/em64t -lmkl_lapack
-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5
current:RP_LIBS:-lmkl_intel_lp64 -lmkl_scalapack_lp64 -lmkl_blacs_lp64
-lmkl_sequential -L /opt/local/fftw/lib/ -lfftw_mpi -lfftw
Even the program works successfully without k-point parallelization, there
could be some mistakes in these options.
_____
Thank you very much for your help in advance, and I am sorry for the
confusions and potential misunderstandings in my previous mail.
Sincerely, Yoo Soo
School of Earth and Environmental Science, Seoul National University, Korea
Yi yoo soo
e-mail: yys2064 at snu.ac.kr OR yiyoosoo at gmail.com
office: +82-2-877-3072
mobile: +82-10-2655-2064
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<div class=3DSection1>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>Dear,
all users.<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'><o:p> </o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>I
am sorry for the multiple postings. In my previous letter, it seems that =
my
questions were not clearly presented. More detailed descriptions of the =
problem
and system specifications are described below. I have been faced with a
problems of calculating ELNES spectrum. <o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'><o:p> </o:p></span></p>
<p class=3DMsoListParagraph =
style=3D'margin-left:38.0pt;mso-para-margin-left:0gd;
text-indent:-18.0pt;mso-list:l0 level1 lfo3'><![if =
!supportLists]><b><span
lang=3DEN-US style=3D'font-family:"Book Antiqua","serif"'><span =
style=3D'mso-list:
Ignore'>(1)<span style=3D'font:7.0pt "Times New =
Roman"'> =
</span></span></span></b><![endif]><b><span
lang=3DEN-US style=3D'font-family:"Book Antiqua","serif"'>Checked =
crystalline system<o:p></o:p></span></b></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>I’ve
calculated a ELENS spectrum using MgO to check whether Wien2k is =
properly compiled
on my system. The tests include, <o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>a)_Single
cell MgO without k-point parallelization option, <o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>b)_single
cell MgO with parallel option,<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>c)_2x2x2
super cell MgO with parallel option, <o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>and
finally d) 2x2x2 super cell without parallel option. =
<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'><o:p> </o:p></span></p>
<p class=3DMsoListParagraph =
style=3D'margin-left:38.0pt;mso-para-margin-left:0gd;
text-indent:-18.0pt;mso-list:l0 level1 lfo3'><![if =
!supportLists]><b><span
lang=3DEN-US style=3D'font-family:"Book Antiqua","serif"'><span =
style=3D'mso-list:
Ignore'>(2)<span style=3D'font:7.0pt "Times New =
Roman"'> =
</span></span></span></b><![endif]><b><span
lang=3DEN-US style=3D'font-family:"Book Antiqua","serif"'>ELNES =
calculation
procedure<o:p></o:p></span></b></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>Used
structural information: MgO structure with 2x2x2 super cell generated =
with
x_supercell<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>Details
of setting (case.in* files): I just followed the setting from the *.pdf =
files
uploaded in web page.<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>init_lapw
(with 1000 k-point, RKmax=3D6.5)<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>edit
case.in1 (increase the energy maximum values to calculate higher energy =
region
in TELNES from default to 4.5 eV)<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>run_lapw
–it (use iterative diagonalization, convergence criteria is set to =
charge
0.0001)<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>telnes
(for Mg K-edge spectrum, setting edge onset, etc., energy grid from 0 eV =
to
35.0 eV)<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>I
did not set the broadening variables (just to check the possibility of =
calculating
spectra)<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>(almost
other variables are used with default values)<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'><o:p> </o:p></span></p>
<p class=3DMsoListParagraph =
style=3D'margin-left:38.0pt;mso-para-margin-left:0gd;
text-indent:-18.0pt;mso-list:l0 level1 lfo3'><![if =
!supportLists]><b><span
lang=3DEN-US style=3D'font-family:"Book Antiqua","serif"'><span =
style=3D'mso-list:
Ignore'>(3)<span style=3D'font:7.0pt "Times New =
Roman"'> =
</span></span></span></b><![endif]><b><span
lang=3DEN-US style=3D'font-family:"Book Antiqua","serif"'>Results from =
test<o:p></o:p></span></b></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>As
test a), we’ve got the result, consistent with the results shown =
in the
Wien2K tutorial (of latest conference file).<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>As
test b), we cannot get the desired result. Instead, the ELNES spectrum =
is
calculated only up to 11 eV (note that we set the energy grid of up to =
35 eV, I
also changed emax value according in the case.in1 file). =
<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>As
test c), it took about 5 days to complete the SCF cycles. It also =
produced the ELNES
spectrum with only up to 11 eV (almost same as result of test =
‘b’).<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>As
test d), a single SCF cycle for the run takes almost 10 hours, and thus =
so I was
forced to quit the job. (I think that it takes too long time to run =
single SCF
cycle comparing with other commercial code that I tested, although they =
are
using different approximation methods defining wave =
functions.)<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'><o:p> </o:p></span></p>
<p class=3DMsoListParagraph =
style=3D'margin-left:38.0pt;mso-para-margin-left:0gd;
text-indent:-18.0pt;mso-list:l0 level1 lfo3'><![if =
!supportLists]><b><span
lang=3DEN-US style=3D'font-family:"Book Antiqua","serif"'><span =
style=3D'mso-list:
Ignore'>(4)<span style=3D'font:7.0pt "Times New =
Roman"'> =
</span></span></span></b><![endif]><b><span
lang=3DEN-US style=3D'font-family:"Book Antiqua","serif"'>Related =
problems of these
results<o:p></o:p></span></b></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>From
those results of parallel computing, there must be some problems using =
k-point
parallelization in my system, even though I tried to modify .machines =
file for
my system (modified files are attached below).<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'><o:p> </o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>Are
there any other parameters (e.g., emax, RMT radii, etc.) that I should =
change
upon the calculation to get the correct results with large size super =
cell? (I could
not find any related comments about dependence of calculation parameters =
on
lattice parameter or number of atoms.)<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'><o:p> </o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>As
for the calculation time, I just wonder whether this could be due to =
some
problems associated with compilation options for my system (see below =
for the details).
<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'><o:p> </o:p></span></p>
<p class=3DMsoListParagraph =
style=3D'margin-left:38.0pt;mso-para-margin-left:0gd;
text-indent:-18.0pt;mso-list:l0 level1 lfo3'><![if =
!supportLists]><b><span
lang=3DEN-US style=3D'font-family:"Book Antiqua","serif"'><span =
style=3D'mso-list:
Ignore'>(5)<span style=3D'font:7.0pt "Times New =
Roman"'> =
</span></span></span></b><![endif]><b><span
lang=3DEN-US style=3D'font-family:"Book Antiqua","serif"'>Other =
questions (about
RAM usage during lapw* calculation)<o:p></o:p></span></b></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>I
set the NMATMAX and NUME parameters as suggested by the Wien2K manual; I =
calculated
these values for a memory size of 24G. <o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'><o:p> </o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>#
NMATMAX =3D sqrt( RAM/10), RAM is the size of memory in =
byte.<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>#
NUME =3D NMATMAX/10<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'><o:p> </o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>However,
when I type ‘top –c’ in the terminal, the RAM usage =
for each single
program, (e.g. lapw1 and lapw2..) is only about 2~3 %. I think this is =
very
low, and thus wonder whether it functions properly or not. However, when =
I use ‘free’
commend, the usage of memory is almost full. Please let me know how this
program controls the memory usage of each single program. =
<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'><o:p> </o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'><o:p> </o:p></span></p>
<div class=3DMsoNormal align=3Dcenter style=3D'text-align:center'><span =
lang=3DEN-US
style=3D'font-family:"Book Antiqua","serif"'>
<hr size=3D2 width=3D"100%" align=3Dcenter>
</span></div>
<p class=3DMsoListParagraph =
style=3D'margin-left:38.0pt;mso-para-margin-left:0gd;
text-indent:-18.0pt;mso-list:l4 level1 lfo5'><![if =
!supportLists]><b><span
lang=3DEN-US style=3D'font-family:"Book Antiqua","serif"'><span =
style=3D'mso-list:
Ignore'>(a)<span style=3D'font:7.0pt "Times New =
Roman"'> =
</span></span></span></b><![endif]><b><span
lang=3DEN-US style=3D'font-family:"Book Antiqua","serif"'>System =
specification<o:p></o:p></span></b></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>CPU:
dual CPU (intel xeon quad core X5550)<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>RAM:
24G<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>OS:
RHE 5.3<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>Compiler:
ifort 11<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>MKL:
intel 10.4<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'><o:p> </o:p></span></p>
<p class=3DMsoListParagraph =
style=3D'margin-left:38.0pt;mso-para-margin-left:0gd;
text-indent:-18.0pt;mso-list:l4 level1 lfo5'><![if =
!supportLists]><b><span
lang=3DEN-US style=3D'font-family:"Book Antiqua","serif"'><span =
style=3D'mso-list:
Ignore'>(b)<span style=3D'font:7.0pt "Times New =
Roman"'> </span></span></span></b><![endif]><b><span
lang=3DEN-US style=3D'font-family:"Book Antiqua","serif"'>Modified =
.machines file<o:p></o:p></span></b></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>1:localhost
(total 8 lines of local host, because the total thread is =
8)<o:p></o:p></span></p>
<p class=3DMsoNormal>…<span lang=3DEN-US =
style=3D'font-family:"Book Antiqua","serif"'><o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>1:localhost<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>granularity:1<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>xxtrafine:1<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'><o:p> </o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>Are
there any things what I have to attach this file? The problems of
parallelization may be come from the misses of this file; and I just =
want to
know that is it possible to use parallelization on my system (SMP) =
without installing
MPI library?<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'><o:p> </o:p></span></p>
<p class=3DMsoListParagraph =
style=3D'margin-left:38.0pt;mso-para-margin-left:0gd;
text-indent:-18.0pt;mso-list:l4 level1 lfo5'><![if =
!supportLists]><b><span
lang=3DEN-US style=3D'font-family:"Book Antiqua","serif"'><span =
style=3D'mso-list:
Ignore'>(c)<span style=3D'font:7.0pt "Times New =
Roman"'> =
</span></span></span></b><![endif]><b><span
lang=3DEN-US style=3D'font-family:"Book Antiqua","serif"'>The =
compilation options
(copied from OPTIONS file)<o:p></o:p></span></b></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>current:FOPT:-FR
-mp1 -w -prec_div -pc80 -pad -align -DINTEL_VML -O3 =
-xSSE4.1<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>current:FPOPT:$(FOPT)<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>current:LDFLAGS:$(FOPT)
-L/opt/intel/mkl/10.2.1.017/lib/em64t -pthread<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>current:DPARALLEL:'-DParallel'<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>current:R_LIBS:-L/opt/intel/mkl/10.2.1.017/lib/em64t
-lmkl_lapack -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core =
-liomp5<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>current:RP_LIBS:-lmkl_intel_lp64
-lmkl_scalapack_lp64 -lmkl_blacs_lp64 -lmkl_sequential -L =
/opt/local/fftw/lib/
-lfftw_mpi -lfftw<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'><o:p> </o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>Even
the program works successfully without k-point parallelization, there =
could be
some mistakes in these options. <o:p></o:p></span></p>
<div class=3DMsoNormal align=3Dcenter style=3D'text-align:center'><span =
lang=3DEN-US
style=3D'font-family:"Book Antiqua","serif"'>
<hr size=3D2 width=3D"100%" align=3Dcenter>
</span></div>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'><o:p> </o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'><o:p> </o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>Thank
you very much for your help in advance, and I am sorry for the =
confusions and potential
misunderstandings in my previous mail.<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'><o:p> </o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>Sincerely,
Yoo Soo<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'><o:p> </o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'><o:p> </o:p></span></p>
<p class=3DMsoNormal><b><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>School
of Earth and Environmental Science, Seoul National University, =
Korea<o:p></o:p></span></b></p>
<p class=3DMsoNormal><b><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>Yi
yoo soo<o:p></o:p></span></b></p>
<p class=3DMsoNormal><b><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>e-mail:
yys2064 at snu.ac.kr OR =
yiyoosoo at gmail.com<o:p></o:p></span></b></p>
<p class=3DMsoNormal><b><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>office:
+82-2-877-3072<o:p></o:p></span></b></p>
<p class=3DMsoNormal><b><span lang=3DEN-US style=3D'font-family:"Book =
Antiqua","serif"'>mobile:
+82-10-2655-2064<o:p></o:p></span></b></p>
<p class=3DMsoNormal><span lang=3DEN-US><o:p> </o:p></span></p>
</div>
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