CentOS7下安装GROMACS（GPU+AVX512）的经历分享

naoki

我大概从去年九月份开始接触一点量化计算和分子动力学模拟，因为课题组是做膜分离方向的，整个组没有任何计算机模拟的经验，开始入门和自学全靠Sob老师的博文、论坛和QQ群了，先感谢一下Sob老师和各位大佬的帮助。对于GROMACS和Linux来说我都只是个新手，长期停留在Windows舒适区，真的会使学习模拟的速度变慢，直到Windows不能满足计算需求，我才开始尝试学习Linux系统。幸运的是我的导师允许我采购一台服务器供课题组计算使用，于是我参考了Sob老师的购机博文《计算化学购机配置推荐》（http://sobereva.com/444），敲定了配置，联系国内某服务器商家采购了一台双路服务器（第一次还是没勇气自己在淘宝上买，现在看来完全不用找这种商家），大致配置如下：

主板：超微X11DAI-N
CPU：Intel Xeon Gold 6148*2
硬盘：4TB 7200RPM SATA 机械 + 500G SSD  
内存：DDR4-2666 ECC 8*16GB   
显卡： NVIDIA RTX2080
机器是CentOS7.3的操作系统，我按照Sob老师帖子《GROMACS的安装方法（含全程视频演示）》（http://bbs.keinsci.com/thread-11821-1-1.html）尝试下载编译安装了GROMACS 2019.1和2018.6两个版本，编译过程一开始挺顺利的，但我想调用AVX512指令集和GPU加速，于是在cmake3那一步额外加了"-DGMX_SIMD=AVX_512"和"-DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda"，然后就提示出错，找不到AVX_512F指令集。后来经排查发现是gcc版本过低所致，CentOS7.3自带gcc的版本是4.8.5（通过执行命令 gcc -v 可以看到），通过官网（GCC 4.8 Release Series https://gcc.gnu.org/gcc-4.8/changes.html）可以查到其支持的微指令集。
gcc4：

可以看到gcc4不支持AVX512。
gcc5：

gcc5开始支持AVX512。
而CUDA从9.0开始支持gcc6.0，CUDA10.0支持gcc6.4，所以gcc不要直接升级到7.X这样的高版本，否则CUDA可能无法支持(CUDA官网可以查看各版本release)。
我是将gcc升级到5.5.0：


wget https://mirrors.ustc.edu.cn/gnu/gcc/gcc-5.5.0/gcc-5.5.0.tar.gz；下载gcc安装包
tar -xf gcc-5.5.0.tar.gz；解压gcc安装包
cd gcc-5.5.0；进入解压后的文件夹
./contrib/download_prerequisites；下载依赖项
mkdir gcc-build-5.5.0；新建gcc-build-5.0.0文件夹
cd gcc-build-5.5.0；进入该文件夹
../configure --enable-checking=release --enable-languages=c,c++ --disable-multilib；设置编译参数：对代码进行一致性检查、支持c和c++语言、我是64位系统，禁止生成32位代码
make -j；开始编译
make install；安装编译好的文件

strings /usr/lib64/libstdc++.so.6|grep GLIBCX；查看/usr/lib64下libstdc++.so.6中包含动态库有哪些版本
strings /usr/local/lib64/libstdc++.so.6|grep GLIBCXX；查看/usr/local/lib64下libstdc++.so.6中包含动态库有哪些版本，更新gcc后/usr/lib64下没有更新动态库，而/usr/local/lib64里有新的库，确认一下
cp /usr/local/lib64/libstdc++.so.6.0.21 /usr/lib64/；所以把更新了的库libstdc++.so.6.0.21复制到/usr/lib64
cd /usr/lib64/；进到/usr/lib64里
rm -f libstdc++.so.6；删掉原来的旧库软链接
ln -s libstdc++.so.6.0.21 libstdc++.so.6；将默认库的软链接指向更新后的动态库
ll libstdc*；查看一下链接成功没

然后在cmake3这一步前加上两步：
export CC=/usr/local/bin/gcc
export CXX=/usr/local/bin/g++

编译就没问题了，本人很菜，如有错误还请大家多多指正~

shuiningzhu

lisanoid 发表于 2021-12-28 17:37
多谢提醒
我重新安装一遍，出现了类似错误，我简单搜索了一下好像是内存不足 ，安装具体信息如下：
/so ...

如果内存够大，swapoff -a，关闭交换分区，否则，扩大交换分区。

lisanoid

snljty 发表于 2021-12-26 05:55
你这个报错没有有价值信息。说清操作所有涉及到的版本和输入，贴更完整的信息。

多谢提醒
我重新安装一遍，出现了类似错误，我简单搜索了一下好像是内存不足 ，安装具体信息如下：
/sob/gcc-5.5.0/gcc-build-5.5.0/./prev-gcc/xg++ -B/sob/gcc-5.5.0/gcc-build-5.5.0/./prev-gcc/ -B/usr/local/x86_64-unknown-linux-gnu/bin/ -nostdinc++ -B/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/src/.libs -B/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/libsupc++/.libs  -I/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/include/x86_64-unknown-linux-gnu  -I/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/include  -I/sob/gcc-5.5.0/libstdc++-v3/libsupc++ -L/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/src/.libs -L/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/libsupc++/.libs -c   -g -O2 -gtoggle -DIN_GCC    -fno-exceptions -fno-rtti -fasynchronous-unwind-tables -W -Wall -Wno-narrowing -Wwrite-strings -Wcast-qual -Wmissing-format-attribute -Woverloaded-virtual -pedantic -Wno-long-long -Wno-variadic-macros -Wno-overlength-strings   -DHAVE_CONFIG_H -I. -I. -I../../gcc -I../../gcc/. -I../../gcc/../include -I../../gcc/../libcpp/include -I/sob/gcc-5.5.0/gcc-build-5.5.0/./gmp -I/sob/gcc-5.5.0/gmp -I/sob/gcc-5.5.0/gcc-build-5.5.0/./mpfr -I/sob/gcc-5.5.0/mpfr -I/sob/gcc-5.5.0/mpc/src  -I../../gcc/../libdecnumber -I../../gcc/../libdecnumber/bid -I../libdecnumber -I../../gcc/../libbacktrace -I/sob/gcc-5.5.0/gcc-build-5.5.0/./isl/include -I/sob/gcc-5.5.0/isl/include  -o ira-color.o -MT ira-color.o -MMD -MP -MF ./.deps/ira-color.TPo ../../gcc/ira-color.c
/sob/gcc-5.5.0/gcc-build-5.5.0/./prev-gcc/xg++ -B/sob/gcc-5.5.0/gcc-build-5.5.0/./prev-gcc/ -B/usr/local/x86_64-unknown-linux-gnu/bin/ -nostdinc++ -B/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/src/.libs -B/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/libsupc++/.libs  -I/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/include/x86_64-unknown-linux-gnu  -I/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/include  -I/sob/gcc-5.5.0/libstdc++-v3/libsupc++ -L/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/src/.libs -L/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/libsupc++/.libs -c   -g -O2 -gtoggle -DIN_GCC    -fno-exceptions -fno-rtti -fasynchronous-unwind-tables -W -Wall -Wno-narrowing -Wwrite-strings -Wcast-qual -Wmissing-format-attribute -Woverloaded-virtual -pedantic -Wno-long-long -Wno-variadic-macros -Wno-overlength-strings   -DHAVE_CONFIG_H -I. -I. -I../../gcc -I../../gcc/. -I../../gcc/../include -I../../gcc/../libcpp/include -I/sob/gcc-5.5.0/gcc-build-5.5.0/./gmp -I/sob/gcc-5.5.0/gmp -I/sob/gcc-5.5.0/gcc-build-5.5.0/./mpfr -I/sob/gcc-5.5.0/mpfr -I/sob/gcc-5.5.0/mpc/src  -I../../gcc/../libdecnumber -I../../gcc/../libdecnumber/bid -I../libdecnumber -I../../gcc/../libbacktrace -I/sob/gcc-5.5.0/gcc-build-5.5.0/./isl/include -I/sob/gcc-5.5.0/isl/include  -o ira-emit.o -MT ira-emit.o -MMD -MP -MF ./.deps/ira-emit.TPo ../../gcc/ira-emit.c
/sob/gcc-5.5.0/gcc-build-5.5.0/./prev-gcc/xg++ -B/sob/gcc-5.5.0/gcc-build-5.5.0/./prev-gcc/ -B/usr/local/x86_64-unknown-linux-gnu/bin/ -nostdinc++ -B/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/src/.libs -B/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/libsupc++/.libs  -I/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/include/x86_64-unknown-linux-gnu  -I/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/include  -I/sob/gcc-5.5.0/libstdc++-v3/libsupc++ -L/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/src/.libs -L/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/libsupc++/.libs -c   -g -O2 -gtoggle -DIN_GCC    -fno-exceptions -fno-rtti -fasynchronous-unwind-tables -W -Wall -Wno-narrowing -Wwrite-strings -Wcast-qual -Wmissing-format-attribute -Woverloaded-virtual -pedantic -Wno-long-long -Wno-variadic-macros -Wno-overlength-strings   -DHAVE_CONFIG_H -I. -I. -I../../gcc -I../../gcc/. -I../../gcc/../include -I../../gcc/../libcpp/include -I/sob/gcc-5.5.0/gcc-build-5.5.0/./gmp -I/sob/gcc-5.5.0/gmp -I/sob/gcc-5.5.0/gcc-build-5.5.0/./mpfr -I/sob/gcc-5.5.0/mpfr -I/sob/gcc-5.5.0/mpc/src  -I../../gcc/../libdecnumber -I../../gcc/../libdecnumber/bid -I../libdecnumber -I../../gcc/../libbacktrace -I/sob/gcc-5.5.0/gcc-build-5.5.0/./isl/include -I/sob/gcc-5.5.0/isl/include  -o ira-lives.o -MT ira-lives.o -MMD -MP -MF ./.deps/ira-lives.TPo ../../gcc/ira-lives.c
/sob/gcc-5.5.0/gcc-build-5.5.0/./prev-gcc/xg++ -B/sob/gcc-5.5.0/gcc-build-5.5.0/./prev-gcc/ -B/usr/local/x86_64-unknown-linux-gnu/bin/ -nostdinc++ -B/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/src/.libs -B/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/libsupc++/.libs  -I/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/include/x86_64-unknown-linux-gnu  -I/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/include  -I/sob/gcc-5.5.0/libstdc++-v3/libsupc++ -L/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/src/.libs -L/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/libsupc++/.libs -c   -g -O2 -gtoggle -DIN_GCC    -fno-exceptions -fno-rtti -fasynchronous-unwind-tables -W -Wall -Wno-narrowing -Wwrite-strings -Wcast-qual -Wmissing-format-attribute -Woverloaded-virtual -pedantic -Wno-long-long -Wno-variadic-macros -Wno-overlength-strings   -DHAVE_CONFIG_H -I. -I. -I../../gcc -I../../gcc/. -I../../gcc/../include -I../../gcc/../libcpp/include -I/sob/gcc-5.5.0/gcc-build-5.5.0/./gmp -I/sob/gcc-5.5.0/gmp -I/sob/gcc-5.5.0/gcc-build-5.5.0/./mpfr -I/sob/gcc-5.5.0/mpfr -I/sob/gcc-5.5.0/mpc/src  -I../../gcc/../libdecnumber -I../../gcc/../libdecnumber/bid -I../libdecnumber -I../../gcc/../libbacktrace -I/sob/gcc-5.5.0/gcc-build-5.5.0/./isl/include -I/sob/gcc-5.5.0/isl/include  -o jump.o -MT jump.o -MMD -MP -MF ./.deps/jump.TPo ../../gcc/jump.c
/sob/gcc-5.5.0/gcc-build-5.5.0/./prev-gcc/xg++ -B/sob/gcc-5.5.0/gcc-build-5.5.0/./prev-gcc/ -B/usr/local/x86_64-unknown-linux-gnu/bin/ -nostdinc++ -B/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/src/.libs -B/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/libsupc++/.libs  -I/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/include/x86_64-unknown-linux-gnu  -I/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/include  -I/sob/gcc-5.5.0/libstdc++-v3/libsupc++ -L/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/src/.libs -L/sob/gcc-5.5.0/gcc-build-5.5.0/prev-x86_64-unknown-linux-gnu/libstdc++-v3/libsupc++/.libs -c   -g -O2 -gtoggle -DIN_GCC    -fno-exceptions -fno-rtti -fasynchronous-unwind-tables -W -Wall -Wno-narrowing -Wwrite-strings -Wcast-qual -Wmissing-format-attribute -Woverloaded-virtual -pedantic -Wno-long-long -Wno-variadic-macros -Wno-overlength-strings   -DHAVE_CONFIG_H -I. -I. -I../../gcc -I../../gcc/. -I../../gcc/../include -I../../gcc/../libcpp/include -I/sob/gcc-5.5.0/gcc-build-5.5.0/./gmp -I/sob/gcc-5.5.0/gmp -I/sob/gcc-5.5.0/gcc-build-5.5.0/./mpfr -I/sob/gcc-5.5.0/mpfr -I/sob/gcc-5.5.0/mpc/src  -I../../gcc/../libdecnumber -I../../gcc/../libdecnumber/bid -I../libdecnumber -I../../gcc/../libbacktrace -I/sob/gcc-5.5.0/gcc-build-5.5.0/./isl/include -I/sob/gcc-5.5.0/isl/include  -o langhooks.o -MT langhooks.o -MMD -MP -MF ./.deps/langhooks.TPo ../../gcc/langhooks.c
make[3]: *** [s-attrtab] Killed
make[3]: *** Waiting for unfinished jobs....
rm gcc.pod
make[3]: Leaving directory `/sob/gcc-5.5.0/gcc-build-5.5.0/gcc'
make[2]: *** [all-stage2-gcc] Error 2
make[2]: Leaving directory `/sob/gcc-5.5.0/gcc-build-5.5.0'
make[1]: *** [stage2-bubble] Error 2
make[1]: Leaving directory `/sob/gcc-5.5.0/gcc-build-5.5.0'
make: *** [all] Error 2

snljty

lisanoid 发表于 2021-12-26 00:48
编译之后报错了，实在太长，最后几行如下：请帮忙分析一下吧
make[3]: *** [s-attrtab] Killed
make[3]:  ...

你这个报错没有有价值信息。说清操作所有涉及到的版本和输入，贴更完整的信息。

lisanoid

编译之后报错了，实在太长，最后几行如下：请帮忙分析一下吧
make[3]: *** [s-attrtab] Killed
make[3]: *** Waiting for unfinished jobs....
rm gcc.pod
make[3]: Leaving directory `/sob/gcc-5.5.0/gcc-build-5.5.0/gcc'
make[2]: *** [all-stage2-gcc] Error 2
make[2]: Leaving directory `/sob/gcc-5.5.0/gcc-build-5.5.0'
make[1]: *** [stage2-bubble] Error 2
make[1]: Leaving directory `/sob/gcc-5.5.0/gcc-build-5.5.0'
make: *** [all] Error 2

snljty

喵星大佬 发表于 2021-4-10 03:11
直接 lscpu就好了

谢谢！当时没仔细查过这类命令，不太熟悉~

hangmint

你这个还好,我遇到了gcc版本过高导致无法编译，也是卸载了原来的gcc重新编译了对应的版本。

喵星大佬

snljty 发表于 2020-10-19 11:20
显示了哪个，就说明支持哪个指令集~

直接 lscpu就好了

lao7

胡说 发表于 2019-4-3 09:39
可以测试下AVX2_256与AVX512的速度差别。
因为我机子上测试发现在GPU加速时候，AVX512要略慢于AVX2_256
...

the tests are very important. Thanks.

jluZ

snljty 发表于 2020-10-19 11:20
显示了哪个，就说明支持哪个指令集~

非常感谢！

snljty

jluZ 发表于 2020-10-19 11:04
非常感谢！
我显示出的是
avx512

显示了哪个，就说明支持哪个指令集~

jluZ

snljty 发表于 2020-10-17 21:04

非常感谢！
我显示出的是
avx512
avx512
avx2
avx2
这种一长串
这样说明是可以的吗？

jluZ

naoki 发表于 2020-10-17 19:52
intel官网

非常感谢！

snljty

jluZ 发表于 2020-10-17 19:20
您知道怎样看自己的cpu适不适合AVX512吗？

1. for i in avx512 avx2 "avx[^2]" sse4_2; do grep -o -e $i /proc/cpuinfo; done

复制代码

naoki

jluZ 发表于 2020-10-17 19:20
您知道怎样看自己的cpu适不适合AVX512吗？

intel官网