Details matter !!! You have to be exact in your description in order
to give us a hint where we can help.
a) How did you install wien2k ??? Did you say a shared memory machine or
not in siteconfig ??
You can check it in $WIENROOT/parallel_options. Both, USE_REMOTE and
MPI_REMOTE should be set to zero for your case.
b) Please copy $WIENROOT/SRC_templates/.machines as a template for a
.machines file and read the instructions about parallelization in the UG.
c) In general I'd most likely set OMP_NUM_THREAD=2 or 4 in your
.bashrc file. This will then use by default 2 (or 4) cores always.
d) Check, understand and test various options in the .machines file.
k-parallel: The syntax is (provided that "localhost" works on your system):
1:localhost
1:localhost
(you cannot type only "localhost" as indicated in your mail). This spans
2 k-parallel jobs, each of them will run on 2 (4) cores due to openMP.
If you add more lines, you span more jobs and can use all your 20 cores.
HOWEVER: This will run 20 times slower for your TiC example, because we
have a short delay between spanning new processes, and this delay is
LONGER than the actual lapw1 job takes.
Alternatively, you could put:
1:localhost:20
omp_global:1
This would not use openMP, but a mpi-job (lapw1_mpi) on 20 cores would
be started. Again, this would run MUCH longer (or even crash ?) for TiC.
In essence: parallelization, and in particular how to parallelize most
efficiently, depends crucial on the SPECIFIC test case. And TiC CANNOT
be efficiently parallelized on 20 cores.
On 8/20/19 7:08 PM, Israel Omar Perez Lopez wrote:
Thanks for your reply
The virtual machine we are using is VMmare esxi 6.0. Linux is installed
in this VM and reconizes the 20 cores Intel(R) Xeon(R) CPU E5-2690 v4 @
2.60GHz, we have 98 GB of RAM, one thread per core, one socket per
core, 20 sockets, and 2 NUMA nodes, 10 cores per node. This is what it
reads from linux terminal.
When a virtual machine is installed, the CPUs are assigned to this VM,
as well as the RAM. There should be no problem with RAM sharing.
Regarding the variable OMP_THREAD, I was mistaken, I wanted to say
OMP_NUM_THREADS; this variable is set to 1 during userconfig. After
executing testpara, only two CPUs are recognized.
I have checked the UG section 5.5 and that is why I tried those options.
I am aware that TiC is a small system, but I used it just to check
parallelization, later I will check timing in the different modes. As of
now I want to make sure how to run the 20 cores in parallel.
So, what is the correct way to configure Wien2k or the .machines file,
so the 20 cores work?
Or is it that parallelization does not work in virtual machines? Has any
one installed Wien2k in a virtual machine?
Regards
Dr. Israel Pérez
Institute of Engineering and Technology
Department of Physics and Mathematics,
Universidad Autónoma de Ciudad Juárez
Av. del Charro 450 Nte., Col. Partido Romero,
Ciudad Juárez, Juarez Chihuahua. Mexico C. P. 32310
Tel: +52 (656) 688 4887
National Council of Science and Technology
Insurgentes Sur No. 1582,
Col. Crédito Constructor, C.P. 03940
Del. Benito Juárez, México D. F.
------------------------------------------------------------------------
*From:* Wien <wien-boun...@zeus.theochem.tuwien.ac.at> on behalf of
Gavin Abo <gs...@crimson.ua.edu>
*Sent:* Tuesday, August 20, 2019 12:05:08 AM
*To:* wien@zeus.theochem.tuwien.ac.at <wien@zeus.theochem.tuwien.ac.at>
*Subject:* Re: [Wien] Installation of wienk
What virtual machine (Virtual Box, VMware, etc. [1])? Seems to matter
according to [2,3].
Since a virtual machine tends to be an operating system running on top
of another operating system (OS), there will most likely be a
performance loss to your calculations [4]. Perhaps the calculation will
run slower [disk caching due to lack of random access memory (RAM), CPU
sharing between both OS) or structures that can be calculated could be
limited by the loss of free RAM (two OS using RAM instead of just one OS
+ RAM used by virtual machine software].
TiC case is fine for first learning mpi parallel but is known that it
can be slower than just doing a serial calculation for it as it is too
small a case (e.g., to few nonequivalent atomic positions) [5,6].
Your statement below "... calculations take longer than in series ..."
seems to confirm this.
"... one processor for the variable OMP_THREAD (instead of 20 cores)
..." <- Don't confuse a thread and a core, they should be different
[7,8,9]. For example, look at the specifications for an i7-8700K
processor [10] which shows that Intel processor has # of cores as 6 and
# of threads as 12.
Is OMP_THREAD a special variable particular to your system? If not, you
might want to check your .bashrc (within the block created by
userconfig_lapw) and the WIEN2k 19.1 UG (section "5.5.3 How to use
WIEN2k as a parallel program" on page 86) [11] as a different
environmental variable might be needed.
username@computername:~$ grep THREAD ~/.bashrc
export OMP_NUM_THREADS=1
[1] https://en.wikipedia.org/wiki/Virtual_machine#Full_virtualization
[2]
https://superuser.com/questions/1035010/what-is-the-performance-difference-of-a-virtual-machine-vs-the-physical-host
[3]
https://www.researchgate.net/post/Why_there_is_a_performance_variation_between_physical_machine_and_virtual_machine_with_same_number_of_cores_and_memory
[4]
https://hetmanrecovery.com/recovery_news/how-to-speed-up-the-operation-of-a-virtual-machine.htm
[5]
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05622.html
[6]
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg02976.html
[7]
https://bitsum.com/tips-and-tweaks/what-is-the-difference-between-a-thread-and-a-core/
[8]
https://www.intel.com/content/www/us/en/architecture-and-technology/hyper-threading/hyper-threading-technology.html
[9]
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08702.html
[10]
https://ark.intel.com/content/www/us/en/ark/products/126684/intel-core-i7-8700k-processor-12m-cache-up-to-4-70-ghz.html
[11] http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf
On 8/19/2019 10:00 PM, Israel Omar Perez Lopez wrote:
Dear mailing list
I have a virtual machine with 20 cores running in linux mint (linux
recognizes that the computer has 20 cores divided in two nodes 10
each, however, there is only one physical node). How can I use Wien2k
to do parallel calculations in a virtual machine so the
parallelization uses the 20 cores. As far as I know, wien2k 19.1 has
three modes of parallelization: MPI, k-point and OMP (according to the
UG only for computers with less than 8 cores). I have already
installed intel parallel studio 2019 and wien2k but when I do the
userconfig the system only detects one processor for the variable
OMP_THREAD (instead of 20 cores). Since it is only one machine, what
is the best configuration in the .machines file to use the 20 cores?
Based on the UG I have tried three configurations for TiC in
.machines: 1) localhost:20, 2) MPI parallelization implemented as:
localhost, localhost, ....localhost 20 times, and 3) k-point
implemented as:
localhost
localhost
....
20 times
For the first and second case, the computations do not stop, it does
not even compute lapw0, so I have to cancel the job with cancel_lapw.
For the third case the calculations are carried out, but it seems that
the 20 cores do not work at the same time, they work one after another
and at the end, thecalculations take longer than in series. I checked
this with testpara1.
I would be glad if you could give a helpful comment on how to use the
20 cores in this machine.
Regards
Dr. Israel Pérez
Institute of Engineering and Technology
Department of Physics and Mathematics,
Universidad Autónoma de Ciudad Juárez
Av. del Charro 450 Nte., Col. Partido Romero,
Ciudad Juárez, Juarez Chihuahua. Mexico C. P. 32310
Tel: +52 (656) 688 4887
National Council of Science and Technology
Insurgentes Sur No. 1582,
Col. Crédito Constructor, C.P. 03940
Del. Benito Juárez, México D. F.
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--
P.Blaha
--------------------------------------------------------------------------
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.at WIEN2k: http://www.wien2k.at
WWW: http://www.imc.tuwien.ac.at/TC_Blaha
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