但是运行后,提示: Fatal error: reading tpx file (md.tpr) version 73 with version 71 program For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors 大概的意思是说:预编译好的mdrun-gpu跑不了由4.5.1版 grompp程序生成的tpr文件。
export OPENMM_ROOT_DIR=path_to_custom_openmm_installation cmake -DGMX_OPENMM=ON [-DCMAKE_INSTALL_PREFIX=desired_install_path] make mdrun make install-mdrun ——————————————————————————
但是新的问题来了, 运行出现错误提示: mdrun-gpu: error while loading shared libraries: libopenmm_api_wrapper.so: cannot open shared object file: No such file or directory 很奇怪! 环境变量也设好了,没有问题 在openmm目录下找不到libopenmm_api_wrapper.so文件
第三天:
我将操作系统换成RHEL5.5系统
再利用相同的安装方法,顺利解决上述问题,
但不明白其中原因,不过我想还是有办法解决的(先不管它)!
第四天:
总结一下我所遇到的问题,及解决办法:
1,版本问题 —————————————————————————— Fatal error: reading tpx file (md.tpr) version 73 with version 71 program For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors 这里是说版本不兼容
2,Openmm不支持多组的温度耦合 —————————————————————————— Fatal error: OpenMM does not support multiple temperature coupling groups. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors
3,不能按以前的mpd来设置 —————————————————————————— Fatal error: OpenMM uses a single cutoff for both Coulomb and VdW interactions. Please set rcoulomb equal to rvdw. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors
4,GPU加速的gmx现在只支持amber力场及charmm力场 —————————————————————————— Fatal error: The combination rules of the used force-field do not match the one supported by OpenMM: sigma_ij = (sigma_i + sigma_j)/2, eps_ij = sqrt(eps_i * eps_j). Switch to a force-field that uses these rules in order to simulate this system using OpenMM.
5,GPU加速的gmx不支持G96里的 interaction ,实际上还是力场问题 —————————————————————————— Fatal error: OpenMM does not support (some) of the provided interaction type(s) (G96Angle) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors
6,在Ubuntu9.10里面用cmake编译gromacs4.5.1会遇到找不到libopenmm_api_wrapper.so文件的问题,换成RHEL5.5可以解决 —————————————————————————— error while loading shared libraries: libopenmm_api_wrapper.so: cannot open shared object file: No such file or directory
It is also possible to optimize the transforms for the current problem by performing some calcula- tions at the start of the run. This is not done by default since it takes a couple of minutes, but for large runs it will save time. Turn it on by specifying optimize_fft = yes
WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator.
WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators.
Pre-simulation ~15s memtest in progress...done, no errors detected starting mdrun 'Protein in water' 1000000 steps, 2000.0 ps.
NODE (s) Real (s) (%) Time: 33.080 99.577 33.2 (Mnbf/s) (MFlops) (ns/day) (hour/ns) Performance: 0.000 0.074 47.609 0.504
gcq#330: "Go back to the rock from under which you came" (Fiona Apple) ———————————————————————————————— 最后这个Performance,有点看不懂,单从(ns/day) 这一点看,性能是l四核心CPU的五倍,但实际运行,性能仅是CPU的2倍, (MFlops) 一项,竟然是 0.074 CPU的 (MFlops) 是12GFlops
5000000 steps, 10000.0 ps. step 417300, will finish Thu Oct 28 10:39:59 2010 /10月18号开始,显示10月28号结束
Received the TERM signal, stopping at the next step
step 417378, will finish Thu Oct 28 10:39:46 2010 Post-simulation ~15s memtest in progress...done, no errors detected
NODE (s) Real (s) (%) Time: 13633.960 71173.931 19.2 3h47:13 (Mnbf/s) (MFlops) (ns/day) (hour/ns) Performance: 0.000 0.003 5.290 4.537
gcq#47: "I Am Testing Your Grey Matter" (Red Hot Chili Peppers)
第七天:
相同的体系,相同的设置,以下是用QX9650 四核心CPU 跑的performance:
性能虽然比GTX460弱,但也只是多算了三天时间 —————————————————————————————— Back Off! I just backed up md.trr to ./#md.trr.1#
Back Off! I just backed up md.edr to ./#md.edr.1#
WARNING: This run will generate roughly 3924 Mb of data
starting mdrun 'Good gRace! Old Maple Actually Chews Slate in water' 5000000 steps, 10000.0 ps. step 0 NOTE: Turning on dynamic load balancing
step 500, will finish Mon Nov 1 09:57:48 2010vol 0.74 imb F 2% /10月19号早上开始,显示的是11月1号结束
Received the TERM signal, stopping at the next NS step
step 550, will finish Mon Nov 1 10:08:34 2010 Average load imbalance: 2.4 % Part of the total run time spent waiting due to load imbalance: 1.1 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: Y 0 %
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%) Time: 123.856 123.856 100.0 2:03 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 156.395 11.835 0.769 31.220
gcq#358: "Now it's filled with hundreds and hundreds of chemicals" (Midlake)