Re: [gmx-users] compile with intel compiler

at. GROMACS automatically looks for the right version of g++ to find the proper version of libstdc++ If you are referring to a different error please be more specific and post the exact error. Roland > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > On Be

[gmx-users] compile with intel compiler

BS”D Dear All, I would like to compile Gromacs 2020 with an intel compiler; I set the following: -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DGMX_MPI=on -DGMX_BUILD_OWN_FFTW=OFF -DGMX_FFT_LIBRARY=mkl -DMKL_LIBRARIES=$MKLROOT/lib/intel64 -DMKL_INCLUDE_DIR=$MKLROOT/include Despite

[gmx-users] syntax error in GMXRC.csh in Gromacs2020

BS”D Seems that a bash formatted line has made it into the csh version of the GMXRC file: setenv GMXTOOLCHAINDIR=${GMXPREFIX}/share/cmake The “=“ should be a space. Harry Harry M. Greenblatt Associate Staff Scientist

[gmx-users] domain decomposition failure

BS”D Dear All, I have now run into this issue with two very different systems (one with 762 protein and 60 DNA residues, the other with 90 protein residues). If I try and carry over the velocities from the final equilibration step into a production run, and try to use more than one MPI

Re: [gmx-users] random initial failure

mdrun -nsteps 0 -nb cpu -pme cpu a few times). -- Szilárd On Mon, Feb 11, 2019 at 11:25 AM Harry Mark Greenblatt mailto:harry.greenbl...@weizmann.ac.il>> wrote: BS”D Dear All, Trying to run a system with about 70,000 atoms, including waters, of a trimeric protein. Went through mini

[gmx-users] random initial failure

BS”D Dear All, Trying to run a system with about 70,000 atoms, including waters, of a trimeric protein. Went through minimization, PT and NPT equilibration. Most of the time, it starts and runs fine. But once in about 5 tries, I get: 12500 steps, 25.0 ps.

Re: [gmx-users] gmx kill computer?

BS”D Dear Michael, ThermalTake PSU’s are better than many out there, but they aren’t the best. Here is a link discussing how the theoretical wattage rating of a PSU may not actually translate into enough watts in reality, especially under sustained load.

Re: [gmx-users] gmx kill computer?

BS”D I had a similar issue with a workstation, and it turned out to be the power supply, which is why it seemed that someone pulled the plug (at least it seems to be the PSU, since having replaced it we don’t see failures). The problem was very intermittent, and did not require any great

[gmx-users] new threadripper

BS”D The newest and most powerful AMD Threadripper, the 2990WX with 32 cores coupled with two powerful GPU’s seems quite attractive, but 2 of the CPU dies are not directly connected to the system memory. Some reviews have warned that this will impact performance under certain workloads, as

Re: [gmx-users] bug in trjconv?

BS”D Dear Mark, did the .tpr actually match the trajectory file? Sorry, that was indeed the problem (mismatch of -f and -s files). Thanks for the hint Harry Harry M. Greenblatt Associate Staff Scientist Dept of

[gmx-users] bug in trjconv?

BS”D In a given system with several chains, after minimisation the chains are split up by PBC. Using trjconv on this file to put all the chains back into a unified complex, the Ions are converted to water molecules. The input file (-f) and the reference file (-s) had waters and Ions

Re: [gmx-users] affect of water removal on subsequent energy calculations

BS”D Ok, thanks for the advice, Harry On 11 Apr 2018, at 11:21 AM, Alex > wrote: Screening effects in Gromacs come in a rather non-straightforward manner in terms of data extraction: they certainly exist within the simulations in the form of

Re: [gmx-users] affect of water removal on subsequent energy calculations

If you plan to extract anything explicitly related to water from your reruns -- very much so. Basically unusable trajectories. Alex On 4/11/2018 1:48 AM, Harry Mark Greenblatt wrote: B”SD In an effort to reduce the size of output xtc files of simulations of large systems, we thought of saving

[gmx-users] affect of water removal on subsequent energy calculations

B”SD In an effort to reduce the size of output xtc files of simulations of large systems, we thought of saving these files without water molecules. It occurred to us, however, that upon subsequent cpu-only reruns in order to do energy calculations, these results would be adversely affected,

Re: [gmx-users] Worse GROMACS performance with better specs?

BS”D Someone has pointed out to me that the “Silver” line is not meant for HPC. For HPC, you need to go with the “Gold” series, even if you don’t want 4 sockets. The difference presumably lies is the fact that the Gold has 2 FMA units, and the Silver series has 1. Harry On 20 Feb 2018,

Re: [gmx-users] how can i restrain Zn ion during simulations

BS”D I am currently running simulations for protein-RNA complex. However i have to include one Zn ion which is coordinated by 4 cysteine residues. when i performed energy minimization itself zinc displaces. How can i restrain to Zn, or to freeze Zn during simulations. You probably should use

Re: [gmx-users] Tests with Threadripper and dual gpu setup

BS”D Did you build with or without hwloc? I did use hwloc. — Gromacs 2018 rc1 (using gcc 4.8.5) — Using AVX_256 You should be using AVX2_128 or AVX2_256 or Zen! The former will be fastest in CPU-only runs, the latter can often be (a bit) faster in GPU

[gmx-users] Tests with Threadripper and dual gpu setup

BS”D In case anybody is interested we have tested Gromacs on a Threadripper machine with two GPU’s. Hardware: Ryzen Threadripper 1950X 16 core CPU (multithreading on), with Corsair H100i V2 Liquid cooling Asus Prime X399-A M/B 2 X Geforce GTX 1080 GPU’s 32 GB of 3200MHz memory Samsung 850 Pro

Re: [gmx-users] new i9 processor

BS”D On 17 Oct 2017, at 1:03 PM, Bernhard Reuter > wrote: Dear Harry, I would assume you are right with your argument that 6/8/10 cores per GPU are better than i.e. 5 cores. If I were you I would still carefully test, if you really have

Re: [gmx-users] new i9 processor

BS”D Dear Bernhard and Szilárd, Since your replies to me are related, I’ll combine my replies to one letter. you are right for the dual xeon 16 core setup you (and we) use, but for the single core i9 setup we made the experience, that we only gained between 5-10% of performance by adding a

[gmx-users] new i9 processor

BS”D Dear All, The new Skylake-X CPU’s have very high core counts, and could, in theory, take the place of a two socket 16 core Xeon system. One could create a machine as follows: 1 x Core i9 7960X with 16 cores 2 x Geforce 1080 graphic cards, and run a simulation with 2 MPI ranks,

Re: [gmx-users] ForceField for Zn

BS”D We have successfully used ZAFF Peters, M., et al., J. Chem. Theory Comput. 20120, 6, 2935-2947. I have the input files from Martin Peters necessary to create additions for the Amber force fields in Gromacs. Which configuration of Zn do you have? Harry On 24 Jul 2017, at 3:18 PM, Erik

Re: [gmx-users] Regarding terminal residue parameters (Capping)

BS”D I am trying to simulate a multichain amino acid structure. PDB ID 2BEG. I am experiencing problems with the C and N terminal residues i. e. C-ALA and N-LEU. An abnormal non-bonded interaction keeps forming between atoms C from ALA42 and N from LEU17. Do you mean from Ala42 of Chain A to

Re: [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?

BSD Dear David and Szilárd Here are the results from our tests: Gromacs 5.0 with AVX2 on E5-2699v3 nodes cores core/socket ns/day wall time, s scaling ideal scaling ideal ns/day 1 12 6 20.023 4315.029 1.00 1.00 20.023 1 16 8 24.912 3468.233 1.24 1.33 26.697 1 20

Re: [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?

BSD Dear David, Hey Harry, Thanks for the caveat. Carsten Kutzner posted these results a few days ago. This is what he said : I never benchmarked 64-core AMD nodes with GPUs. With a 80 k atoms test system using a 2 fs time step I get 24 ns/d on 64 AMD cores 6272 16 ns/d on 32 AMD cores

[gmx-users] modified residues and residual charge

BSD Dear All, I was wondering how people deal with the issue of generating special amino acids in Gaussian, then being left with residual charge upon removing blocking blocks. The process I follow is: 1. Build the modified amino acid (side chain is non-standard) in Gaussian, with

Re: [gmx-users] Illegal instruction flag raised in GMX 5.0.4

BSD Gromacs is telling you that the -h option you supplied is not valid for this command. You can see all the valid arguments for each command here http://manual.gromacs.org/online.html Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology

Re: [gmx-users] avx2 with gcc 4.8.3

BSD Hi, binutils package from this century is required ;-) Mark Thank you. Installation of binutils 2.24 has taken care of the issue. Perhaps mention of the minimum release level of binutils required on the Installation Instructions page is in order. Harry

[gmx-users] avx2 with gcc 4.8.3

BSD Dear All, While trying to run cmake under Centos 6.6 on a Haswell cpu for Gromacs 5.0.3 using gcc 4.8.3, cmake fails claiming the compiler doesn't support AVX2, but as far as I know it should... Cannot find AVX2 compiler flag. Use a newer compiler, or choose AVX SIMD (slower). Some

Re: [gmx-users] avx2 with gcc 4.8.3

BSD Dear Mark, Here is where it fails: -- Try C++ compiler AVX2 flag = [-mavx2] -- Performing Test CXX_FLAG_mavx2 -- Performing Test CXX_FLAG_mavx2 - Success -- Performing Test CXX_SIMD_COMPILES_FLAG_mavx2 -- Performing Test CXX_SIMD_COMPILES_FLAG_mavx2 - Failed -- Try C++ compiler AVX2 flag

Re: [gmx-users] running solvate twice...

BSD Dear Justin, The new water molecules are scattered throughout the box. The density of the system behaves in the following manner 1. First run of solvate: 7025 waters added, density 994.192 g/l (a bit low??) 2. Run solvate on result of 1: 20 waters added, density 996.828 g/l

[gmx-users] running solvate twice...

BSD Dear All, While setting up a system with a small DNA binding domain (30 residues) in close proximity to 9 bp of B DNA, in a dodecahedron box, I ran gmx solvate which added about 7,000 water molecules (spce), followed by addition of 0.125M NaCl. I then minimized this setup, and ran 100ps

Re: [gmx-users] running solvate twice...

BSD Dear Justin, Yes, this is weird. Where are the new waters added? If they're at the periphery, there's probably just some incorrect accounting for PBC, in which case any subsequent run likely shouldn't be stable. The new water molecules are scattered throughout the box. The density

Re: [gmx-users] energy groups rerun from reduced xtc file

, 2014 at 10:16 AM, Harry Mark Greenblatt harry.greenbl...@weizmann.ac.il wrote: BSD Dear All, In an attempt to save disk space while using longer simulations of a DNA + Protein + solvent system, I had mdrun create an xtc file with only the DNA, Protein, and ions, excluding the water

Re: [gmx-users] 1 gpu vs 2 gpu speedup

BSD Dear Szilárd, Thanks very much for your reply. This compiler is very outdated, you should use at least gcc 4.7 or 4.8 for best performance - especially the CPU-only runs should get quite a bit faster. Thanks, point taken. The person who compiled this on the test machine just used what

[gmx-users] 1 gpu vs 2 gpu speedup

BSD Dear All, I was given access to a test machine with 2 x E5-2630 2.3GHz 6 core processors 2 x Tesla K20x GPU's Gromacs 5.0, compiled (gcc 4.4.7) with support for Intel MPI. Ran a 1ns simulation on a 3-domain (all in one chain) DNA binding protein, dsDNA, waters, and ions (~32,600 atoms).

[gmx-users] 1 gpu vs 2 gpu speedup

BSD Dear All, I was given access to a test machine with 2 x E5-2630 2.3GHz 6 core processors 2 x Tesla K20x GPU's Gromacs 5.0, compiled (gcc 4.4.7) with support for Intel MPI. Ran a 1ns simulation on a 3-domain (all in one chain) DNA binding protein, dsDNA, waters, and ions (~32,600 atoms).

Re: [gmx-users] possible configuration for gromacs gpu node

BSD Dear Szilárd, Thanks for your reply. Hence, to get a balanced hardware combination (assuming the same input system and settings), you would need a GPU that's about 2x faster than the K5000. Is that a typo? We used a K4000, with half the number of CUDA cores (768) from what we are

Re: [gmx-users] possible configuration for gromacs gpu node

BSD So a job should run the same or faster on 10 cores at 2.5GHz relative to 6 cores at 3.5GHz? Thanks for letting me know Harry Btw, the 10-core 2.5 Ghz Xeon (2670?) will be a better price/performance - for the same price - as the E5-2643V2, at least for GROMACS and in general codes

[gmx-users] possible configuration for gromacs gpu node

BSD Dear All, I was asked to provide some examples of what we are doing to assess whether my proposal for a GPU compute node is reasonable (2 x 3.5GHz E5-2643V2 hexacore, with 2 x Geforce GTX 770; run two jobs, each with six cores and 1 GPU). I did some tests on a workstation some time ago

Re: [gmx-users] make install creating infinite recursive directories: addendum

BSD Dear Mark, OK. The GROMACS developers intended the user to follow normal practice, such as doing the build in user space in the file system, and then installing as root, and installing to somewhere other than the source tarball location. Unpacking a source tarball in /opt and building from

[gmx-users] make install creating infinite recursive directories

BSD Hi All, I am trying to build 4.6.5 for testing, on a Rocks 5.3 cluster (yes it needs upgrading!). I am using one of the compute nodes to do the compiling, using the following: CMAKE_PREFIX_PATH=/share/apps/fftw-3.3.2 /share/apps/cmake-2.8.12.2/bin/cmake ..

[gmx-users] possible configuration for gromacs gpu compute node

BSD Dear All I was thinking of configuring some GPU compute nodes with the following: 2 x E5-2643v2 (6 cores each, 12 cores total) 2 x GTX 770. The idea is to run two Gromacs jobs on each node, each using 6 cores and 1 GPU card. 1). Does this sound reasonable. 2). If so, I am not clear how