[gmx-users] 3D monitors

2020-01-30 Thread tarzan p 
Hi all..Am looking for some good 3D monitors (either passive or active)Need 
suggestions for some good 3D monitors for protein structure and interactions 
visualization...
with best wishes
-- 
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 gmx-users-requ...@gromacs.org.

[gmx-users] benchmark of RIB

2019-09-02 Thread tarzan p 
Hi allI am sure many of you guys would have run a benchmark of RIB system as 
given https://www.mpibpc.mpg.de/grubmueller/bench


I could manage 12ns/day with a workstation with 2 x Gold 6148 (20 cores each) 
and 2 x V100 GPUs. 
Can you guys post your performance results on a single node with a similar 
configuration

With best wishes
-- 
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 gmx-users-requ...@gromacs.org.

[gmx-users] AVX_512 and GROMACS

2019-08-19 Thread tarzan p 
Hi all.I have a dual socket Xeon GOLD 6148 which has the capabilities for 

 Instruction Set Extensions   Intel® SSE4.2, Intel® AVX, Intel® AVX2, Intel® 
AVX-512
but hen why si gromacs giving the error for AVX_512 but takes AVX2_256???
Adding the out put 


/Downloads/gromacs-2019/build-gromacs$ cmake .. -DGMX_SIMD=AVX_512-- Enabling 
RDTSCP support
-- Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED
-- Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed
-- Performing Test C_xCORE_AVX512_FLAG_ACCEPTED
-- Performing Test C_xCORE_AVX512_FLAG_ACCEPTED - Failed
-- Performing Test C_mavx512f_mfma_FLAG_ACCEPTED
-- Performing Test C_mavx512f_mfma_FLAG_ACCEPTED - Failed
-- Performing Test C_mavx512f_FLAG_ACCEPTED
-- Performing Test C_mavx512f_FLAG_ACCEPTED - Failed
-- Performing Test C_arch_AVX_FLAG_ACCEPTED
-- Performing Test C_arch_AVX_FLAG_ACCEPTED - Failed
-- Performing Test C_hgnu_FLAG_ACCEPTED
-- Performing Test C_hgnu_FLAG_ACCEPTED - Failed
-- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS
-- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed
-- Could not find any flag to build test source (this could be due to either 
the compiler or binutils)
-- Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED
-- Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed
-- Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED
-- Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED - Failed
-- Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED
-- Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED - Failed
-- Performing Test CXX_mavx512f_FLAG_ACCEPTED
-- Performing Test CXX_mavx512f_FLAG_ACCEPTED - Failed
-- Performing Test CXX_arch_AVX_FLAG_ACCEPTED
-- Performing Test CXX_arch_AVX_FLAG_ACCEPTED - Failed
-- Performing Test CXX_hgnu_FLAG_ACCEPTED
-- Performing Test CXX_hgnu_FLAG_ACCEPTED - Failed
-- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS
-- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed
-- Could not find any flag to build test source (this could be due to either 
the compiler or binutils)
CMake Error at cmake/gmxManageSimd.cmake:51 (message):
  Cannot find AVX 512F compiler flag.  Use a newer compiler, or choose a
  lower level of SIMD (slower).
Call Stack (most recent call first):
  cmake/gmxManageSimd.cmake:186 
(gmx_give_fatal_error_when_simd_support_not_found)
  CMakeLists.txt:719 (gmx_manage_simd)


-- Configuring incomplete, errors occurred!
See also 
"/home/gdd/Downloads/gromacs-2019/build-gromacs/CMakeFiles/CMakeOutput.log".
See also 
"/home/gdd/Downloads/gromacs-2019/build-gromacs/CMakeFiles/CMakeError.log".


~/Downloads/gromacs-2019/build-gromacs$ cmake .. -DGMX_SIMD=AVX2_256-- 
Performing Test C_mavx2_mfma_FLAG_ACCEPTED
-- Performing Test C_mavx2_mfma_FLAG_ACCEPTED - Success
-- Performing Test C_mavx2_mfma_COMPILE_WORKS
-- Performing Test C_mavx2_mfma_COMPILE_WORKS - Success
-- Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED
-- Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED - Success
-- Performing Test CXX_mavx2_mfma_COMPILE_WORKS
-- Performing Test CXX_mavx2_mfma_COMPILE_WORKS - Success
-- Enabling 256-bit AVX2 SIMD instructions using CXX flags:  -mavx2 -mfma
-- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED
-- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED - Success
-- The GROMACS-managed build of FFTW 3 will configure with the following 
optimizations: --enable-sse2;--enable-avx;--enable-avx2
-- Configuring done
-- Generating done
-- Build files have been written to: 
/home/gdd/Downloads/gromacs-2019/build-gromacs


-- 
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 gmx-users-requ...@gromacs.org.

[gmx-users] Gromacs-GPU help

2019-08-15 Thread tarzan p 
Hi all,I have started using GROMACS recently on my work station (2 X Intel 6148 
(20 cores each) and 2 x tesla v100 .I have compiled it as per the instructions 
atRun GROMACS 3X Faster on NVIDIA GPUs

| 
| 
| 
|  |  |

 |

 |
| 
|  | 
Run GROMACS 3X Faster on NVIDIA GPUs

Complete your molecular dynamics simulations in hours instead of days. Learn 
more.
 |

 |

 |





I would like to get request for a proper benchmark for GPU version and would 
like to know how to run the GPU version. I mean the command to use one GPU and 
2 GPU(s).
With best wishes
-- 
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 gmx-users-requ...@gromacs.org.

[gmx-users] Gromacs GPU

2019-08-11 Thread tarzan p 
Hi all,I have started using GROMACS recently on my work station (2 X Intel 6148 
(20 cores each) and 2 x tesla v100 .I have compiled it as per the instructions 
atRun GROMACS 3X Faster on NVIDIA GPUs

I would like to get request for a proper benchmark for GPU version and would 
like to know how to run the GPU version. I mean the command to use one GPU and 
2 GPU(s).
With best wishes 

-- 
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 gmx-users-requ...@gromacs.org.