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CentOS7下安装GROMACS(GPU+AVX512)的经历分享

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发布时间: 2019-4-2 15:18

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本帖最后由 naoki 于 2020-9-9 19:28 编辑 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 ...

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shuiningzhu 发表于 Post on 2023-11-15 16:09:21
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 发表于 Post on 2021-12-28 17:37:33
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 发表于 Post on 2021-12-26 05:55:16
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 发表于 Post on 2021-12-26 00:48:58
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 发表于 Post on 2021-4-10 15:23:24

谢谢!当时没仔细查过这类命令,不太熟悉~
hangmint 发表于 Post on 2021-4-10 13:35:56
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 发表于 Post on 2021-4-10 03:11:51
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 发表于 Post on 2021-4-9 22:11:31
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 发表于 Post on 2020-10-20 10:37:15
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 发表于 Post on 2020-10-19 11:20:19
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 发表于 Post on 2020-10-19 11:04:02

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 发表于 Post on 2020-10-19 11:00:03

非常感谢!
snljty 发表于 Post on 2020-10-17 21:04:10
本帖最后由 snljty 于 2020-10-17 21:08 编辑
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 发表于 Post on 2020-10-17 19:52:30
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?

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