Re: [gmx-users] V2018.1 building issues

dware flavor and have the module system choose the correct one to > load, per our installation guide > http://manual.gromacs.org/documentation/2018/install- > guide/index.html#portability-aspects > > > Mark > > On Thu, May 10, 2018 at 4:17 PM kevin chen <fch6...@gmail.

[gmx-users] V2018.1 building issues

Hi Gromacs Users, I'm having this weird issue while trying to build the new V2018.1 on Stampede2, which has both SKX amd KNL nodes on it. For V2016 and older, in order to run the same executable(mdrun_mpi), we have to build the "fat" binary with " -DGMX_SIMD=AVX_512" and "-DCMAKE_C_FLAGS="-O3

[gmx-users] Errors while building with Cuda 9.0

Dear Gromacs Users, I got the following error while building V2016.3 using CudaV9.0. Anybody has a quick fix for it? == "nvcc fatal : Unsupported gpu architecture 'compute_20' nvcc fatal : Unsupported gpu

[gmx-users] GPU ECC question

to know (and have references for) 1) How often these errors occur? 2) Can Gromacs along with ECC detect and correct for these errors? 3) How robust are the algorithms governing MD against these types of errors? 4) Is the time and resource overhead from ECC even worth it? Thanks in advance! Kevin Chen

[gmx-users] Issues with huge system

Hi Gromacs Users, We 've observed some issues while creating huge simulation boxes (over35 nm* 35 nm * 35nm in size). Commands used for building our benchmarks showed as follow: gmx pdb2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce gmx editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro

[gmx-users] mdrun_mpi nice level

Dear all, It appears that as of V5.1, the -nice option is no longer supported and the default nice level(19) was used. Is there any reason behind of this? And what's the best way to control mdrun nice level in V5.1? Thanks, Kevin -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Gromacs 5.0 benchmarks

and tprs) used for those benchmarks? We'd like to see if we could reproduce any of those results. Thank you in advance! Kevin Chen -- 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

[gmx-users] Gromacs 5.1 benchmarks

? Thanks, Kevin Chen -- 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

[gmx-users] Building gromacs on CRAY XC40

Dear Gromacs users, I am trying to build gromacs on our latest supercomputer CRAY XC40, but the following errors using gcc and fftw. Here's my list of module loaded and install script, can anyone give any instructions? =

[gmx-users] running g_tune_pme on stampede

suggestion is welcome! Thanks in advance Kevin Chen -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Szilárd Páll Sent: Friday, December 5, 2014 12:54 PM To: Discussion list for GROMACS

[gmx-users] ngmx removed in 5.0.1?

Hi, I just noticed that the ngmx is no longer available in V5.0.1 anymore. Is there another tool can be used as a replacement of ngmx? Or you guys just plan to get rid of it for good? Thanks, Kevin Chen -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org