GROMACS的安装方法（含全程视频演示）

rice · 发表于 Post on 2021-1-1 03:47:48

本帖最后由 rice 于 2021-1-1 03:58 编辑

卢老师，我按照帖子的方式安装2019.6、2019.4，总是失败。试过用户和管理员，都不行。cmake版本为3.9.2。自己下载傅里叶变换库和按帖子中注1提到的自动下载，cmake期间均是出现图示错误，

没法到最后一步。系统为CentOS 7.6。电脑已经装了CUDA10.1，

，按照老师说的在camke时加上路径，和不加时报错一致。请问您和其他老师有什么建议呢？

rice · 发表于 Post on 2021-1-1 11:43:44

rice 发表于 2021-1-1 03:47
卢老师，我按照帖子的方式安装2019.6、2019.4，总是失败。试过用户和管理员，都不行。cmake版本为3.9.2。自 ...

问题已经解决了，在cmake部分额外添加-DGMX_SIMD=AVX2_256，就可以正常编译安装了

tjuptz · 发表于 Post on 2021-1-8 21:11:42

注：对于有GPU和CUDA驱动的机器，即便不加-DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda选项，也会自动尝试编译GPU版本。如果不想编译GPU的，用-DGMX_GPU=off关掉。
另外，即便是GPU版本的，应该也可以通过mdrun的 -nb cpu -pme cpu -bonded cpu（2018.8没有-bonded 选项）来关闭GPU；如果是孤立分子体系pbc=no，不用上述选项应该也会自动关闭GPU的使用。
也就是说，GPU机器似乎不用重新编译非GPU版本吧。

Bergen · 发表于 Post on 2021-1-22 20:44:45

老师我在运行cmake3 .. -DCMAKE_INSTALL_PREFIX=/sob/gmx2018.4
显示
CMake Error: The source directory "/sob/gromacs-2018.4" does not appear to contain CMakeLists.txt.

Specify --help for usage, or press the help button on the CMake GUI.
请问这是什么问题

sobereva · 发表于 Post on 2021-1-23 06:44:16

Bergen 发表于 2021-1-22 20:44
老师我在运行cmake3 .. -DCMAKE_INSTALL_PREFIX=/sob/gmx2018.4
显示
CMake Error: The source director ...

路径弄错了，严格参照帖子编译

sobereva · 发表于 Post on 2021-1-31 18:59:04

经测试，此文安装方法对于新发布的GROMACS 2021依然适用，但需要用较新的cmake，在文中已增加了说明

abicaizhan · 发表于 Post on 2021-3-31 11:52:33

SOB老师，目前我按照您这边的教程，安装GPU版的Gromacs,遇到的问题见下，您这边有什么解决思路或是方案么？

[root@gpumaster build]# export CMAKE_PREFIX_PATH=/home/zbc/fftw338
[root@gpumaster build]# cmake3 .. -DCMAKE_INSTALL_PREFIX=/home/zbc/gmx2019.4 -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
CMake Warning (dev) at /usr/share/cmake3/Modules/FindPackageHandleStandardArgs.cmake:272 (message):
  The package name passed to `find_package_handle_standard_args` (pygments)
  does not match the name of the calling package (Sphinx).  This can lead to
  problems in calling code that expects `find_package` result variables
  (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
  cmake/FindPythonModule.cmake:76 (find_package_handle_standard_args)
  cmake/FindSphinx.cmake:73 (find_python_module)
  docs/CMakeLists.txt:71 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Configuring done
-- Generating done
-- Build files have been written to: /opt/gromacs-2019.4/build
[root@gpumaster build]# make install -j
[  0%] Building NVCC (Device) object src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utilstest_cuda.dir/gpu_utilstest_cuda_generated_devicetransfers.cu.o
[  1%] Built target libgromacs_external
[  1%] Built target lmfit_objlib
[  3%] Built target tng_io_obj
[  3%] Built target tng_io_zlib
[  3%] Built target mdrun_objlib
[  3%] Built target view_objlib
nvcc fatal : Unsupported gpu architecture 'compute_30'
CMake Error at gpu_utilstest_cuda_generated_devicetransfers.cu.o.Release.cmake:220 (message):
  Error generating
  /opt/gromacs-2019.4/build/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utilstest_cuda.dir//./gpu_utilstest_cuda_generated_devicetransfers.cu.o

make[2]: *** [src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utilstest_cuda.dir/gpu_utilstest_cuda_generated_devicetransfers.cu.o] Error 1
[  5%] Built target mdrun_test_objlib
make[1]: *** [src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utilstest_cuda.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 31%] Built target libgromacs_generated
make: *** [all] Error 2

sobereva · 发表于 Post on 2021-3-31 12:21:48

abicaizhan 发表于 2021-3-31 11:52
SOB老师，目前我按照您这边的教程，安装GPU版的Gromacs,遇到的问题见下，您这边有什么解决思路或是方案么？ ...

CUDA toolkit版本兼容性问题。换个较新的CUDA toolkit结合较新的GROMACS版本再试

牧生 · 发表于 Post on 2021-3-31 12:23:49

abicaizhan 发表于 2021-3-31 11:52
SOB老师，目前我按照您这边的教程，安装GPU版的Gromacs,遇到的问题见下，您这边有什么解决思路或是方案么？ ...

似乎你只解压了FFTW，并没有安装？？？

abicaizhan · 发表于 Post on 2021-3-31 14:38:43

本帖最后由 abicaizhan 于 2021-3-31 16:55 编辑

好的，谢谢SOB老师，目前我尝试了cuda11.1和不同版本的groamcs（2019.4,2020.4,2021.1）,2019.4和2021.1报错和之前的一样，没啥变化。

2020.4的报错见下：
root@gpumaster gromacs-2020.4]# cd build/
[root@gpumaster build]# gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/opt/rh/devtoolset-7/root/usr/libexec/gcc/x86_64-redhat-linux/7/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --enable-bootstrap --enable-languages=c,c++,fortran,lto --prefix=/opt/rh/devtoolset-7/root/usr --mandir=/opt/rh/devtoolset-7/root/usr/share/man --infodir=/opt/rh/devtoolset-7/root/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --enable-plugin --with-linker-hash-style=gnu --enable-initfini-array --with-default-libstdcxx-abi=gcc4-compatible --with-isl=/builddir/build/BUILD/gcc-7.3.1-20180303/obj-x86_64-redhat-linux/isl-install --enable-libmpx --enable-gnu-indirect-function --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 7.3.1 20180303 (Red Hat 7.3.1-5) (GCC)
[root@gpumaster build]# export CMAKE_PREFIX_PATH=/opt/fftw338
[root@gpumaster build]# cmake3 .. -DCMAKE_INSTALL_PREFIX=/opt/gmx2020.4 -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-11.1
CMake Error at cmake/gmxTestCompilerProblems.cmake:72 (message):
  GCC version 5 or later required.  Earlier versions don't have full C++14
  support.
Call Stack (most recent call first):
  CMakeLists.txt:345 (gmx_test_compiler_problems)

-- Configuring incomplete, errors occurred!
See also "/opt/gromacs-2020.4/build/CMakeFiles/CMakeOutput.log".
See also "/opt/gromacs-2020.4/build/CMakeFiles/CMakeError.log".

很奇怪，gcc的版本升级了也没解决这个问题

abicaizhan · 发表于 Post on 2021-3-31 16:57:15

牧生发表于 2021-3-31 12:23
似乎你只解压了FFTW，并没有安装？？？

fftw安装好了，非GPU版本的gromacs也是用的这个fftw，测试过是可用的

rpestana94 · 发表于 Post on 2021-4-22 06:30:55

Professor Sob, one question, if I want both version (gpu and cpu) at the same time, how should be the bash file, if I do this "source /sob/gmx2018.8/bin/GMXRC" for the both version I assumed just the last one will actually take effects or just one of these can be installed?

sobereva · 发表于 Post on 2021-4-23 00:07:48

rpestana94 发表于 2021-4-22 06:30
Professor Sob, one question, if I want both version (gpu and cpu) at the same time, how should be th ...

Although you can install both versions, they cannot be simultaneously activated, only one can be used.
In fact, you can always use GPU version, when running on CPU is needed you can add corresponding mdrun options. For example, adding -nb cpu -pme cpu -bonded cpu

rpestana94 · 发表于 Post on 2021-4-23 03:58:57

sobereva 发表于 2021-4-22 11:07
Although you can install both versions, they cannot be simultaneously activated, only one can be u ...

Thanks

pcxlm1 · 发表于 Post on 2021-5-5 23:43:14

h840473807 发表于 2019-3-8 10:10
你的问题解决了吗？我也是类似的情况，在CentOS 6的机子上安装，报错提示我的gcc是4.4.1的，版本不够，可 ...

老师您好，我按照您说的加了两行代码，还是出现与xaomidaxue网友同样的错误，显示CMake Error at cmake/gmxTestCXX11. cmake:135(message): GROMACS requires version 4.8.1 or later of the GNU C++ compiler for complete C++11 support

我的gcc版本是6.4.0, linux 版本是CentOS 6.9

请问您是怎么编译成功的？是不是centos 6安装不了2018版本啊?

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[GROMACS] GROMACS的安装方法（含全程视频演示）