Nour

[nour heikal]

Hi I am Nour , New user to nwchem , I am using nwchem on a HPC with 48 core , 256 GB RAM , 8 Numa Nodes , i have a problem understanding th memory allocations on NWchem documentation and choosing one for my calculations my single point and optmization calculations take way to long and only takes 11 gb of ram even though i use , memory stack 13500 mb heap 13000 mb global 230000 mb config , and i use and sjob file for run containing  mpirun --allow-run-as-root -np $2 numactl --interleave=all /usr/bin/nwchem $1.nw > $1.out & , here is the OPT code i use below  , what should I do .

[Edoardo Aprà]

If you are a new user to NWChem, you might want to try smaller molecules first and have a look at the NWChem website https://nwchemgit.github.io for guidance.

I would also suggest you to avoid running application as root user.

[nour heikal]

thank you so much for getting back to me!

 i did run small molecule but with a desktop configuration , my first time as using HPC to run it , I have a bit of guidence but these memory allocation arents what we really get which configuration is the best to reduce run time i run my optmizations succesfully but just i use minimal Ram for it 

[Edoardo Aprà]

My suggestion is to try first the cheaper PBE functional as in attached input that uses the CD fitting approach to  speed up the calculation

[nour heikal]

thank you so much professor this was a really helpful advise , can I ask whether there is any way where i can maximize RAM usage as well

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[Edoardo Aprà]

There is not a generic way to maximize the memory usage in NWChem. The memory input line simply put an upper bound in the memory usage and, depending on the modules and computational parameters, NWChem memory usage will vary.

Using the input I posted yesterday as an example, we could focus on the memory usage for the Coulomb potential evaluation using the CD fitting approach. In this case, if enough memory is available, NWChem will store the 3-center integrals (the most computational expensive data for this step) in memory. You could check the following line in the output file by searching for the "3-center" string. In the line below, the NWChem run was able to store all the integrals by using  176.421 MegaWords (around 1.4GB) on each process

         176.421 MW buffer allocated for incore 3-center

I hope this example is clear to show that around 1.4GB is the maximum amount of memory that could be used for this specific case. In other words, if you provide x amount of memory in the input line, do not expect NWChem to use 100% of it since its usage varies.