使用conda安装openmpi编译nwchem

conda安装openmpi编译nwchem"/>

使用conda安装openmpi编译nwchem

1 遇到如下错误:找不到libpthread.so.0

configure:20418: checking whether FLIBS needs -lgcc_s
configure:20443: cc -o conftest -m64 -Wall -O3 -funroll-loops -ffast-math  -fopenmp -g  -I.  -I/home/apps/jinrf/nwchem-conda/nwchem/src/include -I/home/apps/jinrf/nwchem-conda/nwchem/src/tools/install/include -DGFORTRAN -DCHKUNDFLW -DGCC4 -DGCC46 -DEXT_INT -DLINUX -DLINUX64 -DUSE_OPENMP -DPARALLEL_DIAG -DTCE_CUDA -DOPENBLAS  -fopenmp -L/home/apps/jinrf/nwchem-conda/nwchem/lib/LINUX64 -L/home/apps/jinrf/nwchem-conda/nwchem/src/tools/install/lib  conftest.c -lm   -L/home/apps/jinrf/nwchem-conda/nwchem/lib/LINUX64 -L/home/apps/jinrf/nwchem-conda/nwchem/src/tools/install/lib -L/home/apps/jinrf/tools/anaconda3/envs/ompi/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0 -L/home/apps/jinrf/tools/anaconda3/envs/ompi/bin/../lib/gcc -L/home/apps/jinrf/tools/anaconda3/envs/ompi/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/lib/../lib -L/home/apps/jinrf/tools/anaconda3/envs/ompi/bin/../x86_64-conda-linux-gnu/sysroot/lib/../lib -L/home/apps/jinrf/tools/anaconda3/envs/ompi/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib -L/home/apps/jinrf/tools/anaconda3/envs/ompi/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/lib -L/home/apps/jinrf/tools/anaconda3/envs/ompi/bin/../x86_64-conda-linux-gnu/sysroot/lib -L/home/apps/jinrf/tools/anaconda3/envs/ompi/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib -lgfortran -lm -lgomp -lquadmath -lpthread >&5
/usr/bin/ld: cannot find /lib64/libpthread.so.0
/usr/bin/ld: cannot find /usr/lib64/libpthread_nonshared.a
collect2: error: ld returned 1 exit status
configure:20443: $? =

使用find命令在anaconda中查找.当前用的conda环境是ompi

apps@dgx-a100:~/jinrf/tools$ find ./ -name "*libpthread*"
./anaconda3/envs/gcc9/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/libpthread_nonshared.a
./anaconda3/envs/gcc9/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/libpthread.so
./anaconda3/envs/gcc9/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/libpthread.a
./anaconda3/envs/gcc9/x86_64-conda_cos6-linux-gnu/sysroot/lib/libpthread.so.0
./anaconda3/envs/gcc9/x86_64-conda_cos6-linux-gnu/sysroot/lib/libpthread-2.12.2.so
./anaconda3/envs/ompi/x86_64-conda-linux-gnu/sysroot/usr/lib64/libpthread_nonshared.a
./anaconda3/envs/ompi/x86_64-conda-linux-gnu/sysroot/usr/lib64/libpthread.so
./anaconda3/envs/ompi/x86_64-conda-linux-gnu/sysroot/lib64/libpthread.so.0
./anaconda3/envs/ompi/x86_64-conda-linux-gnu/sysroot/lib64/libpthread-2.12.so
./anaconda3/pkgs/gcc_impl_linux-64-7.3.0-habb00fd_1/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/libpthread_nonshared.a
./anaconda3/pkgs/gcc_impl_linux-64-7.3.0-habb00fd_1/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/libpthread.so
./anaconda3/pkgs/gcc_impl_linux-64-7.3.0-habb00fd_1/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/libpthread.a
./anaconda3/pkgs/gcc_impl_linux-64-7.3.0-habb00fd_1/x86_64-conda_cos6-linux-gnu/sysroot/lib/libpthread.so.0
./anaconda3/pkgs/gcc_impl_linux-64-7.3.0-habb00fd_1/x86_64-conda_cos6-linux-gnu/sysroot/lib/libpthread-2.12.2.so
./anaconda3/pkgs/gcc_impl_linux-64-7.3.0-hd420e75_5/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/libpthread_nonshared.a
./anaconda3/pkgs/gcc_impl_linux-64-7.3.0-hd420e75_5/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/libpthread.so
./anaconda3/pkgs/gcc_impl_linux-64-7.3.0-hd420e75_5/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/libpthread.a
./anaconda3/pkgs/gcc_impl_linux-64-7.3.0-hd420e75_5/x86_64-conda_cos6-linux-gnu/sysroot/lib/libpthread.so.0
./anaconda3/pkgs/gcc_impl_linux-64-7.3.0-hd420e75_5/x86_64-conda_cos6-linux-gnu/sysroot/lib/libpthread-2.12.2.so
./anaconda3/pkgs/sysroot_linux-64-2.12-h77966d4_13/x86_64-conda-linux-gnu/sysroot/usr/lib64/libpthread_nonshared.a
./anaconda3/pkgs/sysroot_linux-64-2.12-h77966d4_13/x86_64-conda-linux-gnu/sysroot/usr/lib64/libpthread.so
./anaconda3/pkgs/sysroot_linux-64-2.12-h77966d4_13/x86_64-conda-linux-gnu/sysroot/lib64/libpthread.so.0
./anaconda3/pkgs/sysroot_linux-64-2.12-h77966d4_13/x86_64-conda-linux-gnu/sysroot/lib64/libpthread-2.12.so

可以看到其中的一行为

/anaconda3/envs/ompi/x86_64-conda-linux-gnu/sysroot/lib64/libpthread.so.0

这表明,在ompi环境中是有libthread.so.0的,只不过是在sysroot/lib64/目录下,而从出错信息中可以看到,编译器的哭文件搜索路径只有sysroot/lib。