On 7/13/19 7:56 AM, kalpana wrote:
Hi everyone,
I installed gromacs with following configuration still my am getting
suggestion mentioned bellow during mdrun. I used previous following command
to restart. I used to use command (gmx mdrun md_0_1.tpr -deffnm md_0_1 -cpi
md_0_1.cpt -append) at sudden power breakdown. But it gives error. So
given the situation, I have two questions:
Q1. how to update configuration after installation as re-installation
didn't help in this case.
Q2. what is the difference between in both these two commands, I used one
year back at the time of sudden break. Now I have forgotten and both are
giving error.
gmx mdrun md_0_1.tpr -deffnm md_0_1 -cpi md_0_1.cpt -append
gmx mdrun deffnm -s md_0_1.tpr -cpi md_0_1.cpt -append
Neither of those commands is syntactically correct.
gmx mdrun -deffnm md_0_1 -cpi -append
*Cmake configuration*
sudo cmake .. -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=OFF
-DCMAKE_C_COMPILER=gcc -DGMX_MPI=on -DGMX_USE_RDTSCP=ON -DGMX_GPU=on
-DGMX_SIMD=AVX2_256 -DGMX_FFT_LIBRARY=fftw3
-DREGRESSIONTEST_PATH=/gromacs/regressiontests-2019.3
*Suggestion during MDRUN*
Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see
log).
Here, mdrun is telling you that it is slower than it could be on the
given hardware. You should let cmake automatically find the best SIMD
optimization.
The current CPU can measure timings more accurately than the code in
gmx mdrun was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake
option.
Again, use this setting when compiling.
Neither of these messages will halt mdrun. They are merely advising you
that you are not getting the best possible performance.
-Justin
Reading file em.tpr, VERSION 2019.3 (single precision)
Thanks & best regards,
Kalpana
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
[email protected] | (540) 231-3129
http://www.thelemkullab.com
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to [email protected].
