[Wien] Installation of wienk

Tue Aug 20 19:08:48 CEST 2019

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-bounces at zeus.theochem.tuwien.ac.at> on behalf of Gavin Abo <gsabo at crimson.ua.edu>
Sent: Tuesday, August 20, 2019 12:05:08 AM
To: wien at zeus.theochem.tuwien.ac.at <wien at 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 at 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, the calculations 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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