编译OpenMPI4.1.1时出现错误

andycheng2026

小白在按照 http://bbs.keinsci.com/thread-11697-1-1.html 的方法安装OpenMPI4.1.1时，运行make all install 后出现以下错误：

collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:1880: opal_wrapper] Error 1
make[2]: Leaving directory '/home/ubuntu/Downloads/openmpi-4.1.1/opal/tools/wrappers'
make[1]: *** [Makefile:2383: all-recursive] Error 1
make[1]: Leaving directory '/home/ubuntu/Downloads/openmpi-4.1.1/opal'
make: *** [Makefile:1901: all-recursive] Error 1

请问该如何解决？谢谢！

sobereva

看编译过程产生的日志文件末尾提示的信息试图判断

andycheng2026

文件末尾如下：
make[2]: Entering directory '/home/ubuntu/Downloads/openmpi-4.1.1/opal/tools/wrappers'
  CCLD     opal_wrapper
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_bitmap_last'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_libevent2022_evthread_use_pthreads'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_topology_get_support'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_libevent2022_event_base_loop'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_bitmap_dup'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_bitmap_isincluded'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_set_area_membind'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_bitmap_copy'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_topology_destroy'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_bitmap_list_asprintf'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_bitmap_or'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_obj_type_string'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_bitmap_set'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_libevent2022_event_add'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_obj_type_snprintf'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_topology_export_xmlbuffer'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_bitmap_isfull'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_get_type_depth'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_libevent2022_event_base_free'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_shmem_topology_adopt'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_libevent2022_event_base_loopbreak'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_topology_load'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_topology_set_xml'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_set_membind'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_bitmap_isset'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_bitmap_iszero'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `mca_event_libevent2022_component'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_bitmap_list_sscanf'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_bitmap_intersects'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_get_depth_type'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_libevent2022_event_priority_set'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_topology_init'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_bitmap_snprintf'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_topology_get_depth'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_bitmap_free'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_topology_set_flags'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_libevent2022_event_del'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_bitmap_first'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_libevent2022_event_assign'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_obj_attr_snprintf'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_bitmap_alloc'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_get_obj_by_depth'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_distances_release'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_topology_set_io_types_filter'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_libevent2022_event_base_priority_init'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_distances_get_by_depth'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_bitmap_zero'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `mca_hwloc_hwloc201_component'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_topology_dup'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_topology_set_xmlbuffer'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_get_nbobjs_by_depth'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_get_cpubind'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_libevent2022_event_reinit'
/usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference to `opal_hwloc201_hwloc_bitmap_weight'
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:1880: opal_wrapper] Error 1
make[2]: Leaving directory '/home/ubuntu/Downloads/openmpi-4.1.1/opal/tools/wrappers'
make[1]: *** [Makefile:2383: all-recursive] Error 1
make[1]: Leaving directory '/home/ubuntu/Downloads/openmpi-4.1.1/opal'
make: *** [Makefile:1901: all-recursive] Error 1

不懂是什么原因导致。

zjxitcc

试试用Intel编译器编译openmpi，即一开始
./configure --prefix=你要的安装路径 FC=ifort F77=ifort CC=icc CXX=icpc

sobereva

andycheng2026 发表于 2021-10-19 08:20
文件末尾如下：
make[2]: Entering directory '/home/ubuntu/Downloads/openmpi-4.1.1/opal/tools/wrapper ...

说明当前用的是什么编译器

andycheng2026

sobereva 发表于 2021-10-20 03:09
说明当前用的是什么编译器

应该是gcc和g++，因为编译过程中提示安装了。

andycheng2026

zjxitcc 发表于 2021-10-20 01:14
试试用Intel编译器编译openmpi，即一开始
./configure --prefix=你要的安装路径 FC=ifort F77=ifort CC=ic ...

会出现如下报错：
*** Startup tests
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for gcc... icc
checking whether the C compiler works... no
configure: error: in `/home/ubuntu/Downloads/openmpi-4.1.1':
configure: error: C compiler cannot create executables
See `config.log' for more details

zjxitcc

andycheng2026 发表于 2021-10-20 05:23
会出现如下报错：
*** Startup tests
checking build system type... x86_64-pc-linux-gnu

你能截图说明你的运行命令么？我感觉你不是按我说的那么运行的。另外，先运行
ifort --version
icc --version
icpc --version
如果这三个显示找不到，说明你机子上没有intel编译器，自然也就没法使用其编译openmpi

九曜

zjxitcc 发表于 2021-10-20 10:31
你能截图说明你的运行命令么？我感觉你不是按我说的那么运行的。另外，先运行
ifort --version
icc --v ...

请问师兄：
1.如果编译openmpi的时候，module load 加载了 gcc/gcc-8.3.0 是不是就已经默认指定了CC=gcc CXX=g++ FC=gfortran。
2.如果这时候我再想编译一个xxx.f90文件，指定了FC=mpi90，他会报错Fatal Error: File 'mpi.mod' opened at (1) is not a GNU Fortran module file。mpi90 --show 显示使用的是gfortran，是不是用gfortran就无法加载这个mpi.mod库呢，需要改成ifort才可以么。具体应该怎么修改呢，需要重新编译openmpi 指定FC=ifort么。
3.我已经用现在的openmpi安装了block2，如果用intel 编译器重新编译openmpi，我的block2还需要重新编译一次么。

zjxitcc

九曜 发表于 2023-3-31 20:26
请问师兄：
1.如果编译openmpi的时候，module load 加载了 gcc/gcc-8.3.0 是不是就已经默认指定了CC=gcc C ...

1. 不是。
2. 我没见过指定FC=mpif90的，一般来说比较完善的程序的configure/Makefile/CMakeLists.txt会认MPIF90之类变量的值为MPI编译器，而FC变量仍留给ifort或gfortran。另外，FC与MPIF90的值建议具有一致性，例如当FC=ifort时，MPIF90最好采用Intel编译器编译的openmpi，而非GNU编译的openmpi。
建议阅读一下程序安装说明。（当然，如果是自己写的程序，那是想怎么指定就怎么指定，只不过不太符合传统约定）
3. 是的。但我没见过/试过用Intel编译的openmpi去编译block2是否可以。所以比较好的办法是将环境变量写在提交任务的脚本里，要啥写啥。安装block2可参考我写的《block2的编译和安装》

算量子

1. 安装基础依赖
sudo yum install -y gcc gcc-c++ gcc-gfortran make automake libtool
sudo yum install -y openssl-devel zlib-devel hwloc-devel libevent-devel
2. 清理并重新配置
cd /路径/openmpi416（存放openmpi的文件夹路径）
make distclean
./configure --prefix=/path/to/install/dir
3. 检查编译器兼容性
sudo yum install -y centos-release-scl
sudo yum install -y devtoolset-8
scl enable devtoolset-8 bash
4. 检查环境变量冲突
(将环境变量.bashrc文件中关于openmpi的配置全部删掉或者首行打#备注掉)
确保环境变量未干扰编译：
unset LD_LIBRARY_PATH
export C_INCLUDE_PATH=/usr/include:/usr/local/include
export LIBRARY_PATH=/usr/lib:/usr/local/lib
5. 编译调试
./configure --prefix=/路径/openmpi416 --disable-builtin-atomics
make all install
6. 重新编辑openmpi变量环境
#OpenMPI
export PATH=$PATH:/路径/openmpi416/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/路径/openmpi416/lib
export OMPI_ALLOW_RUN_AS_ROOT=1
export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
7. 验证安装：
运行mpiexec -V命令，显示出了OpenMPI的版本

Centos7 停止维护之后 升级gcc||找不到devtoolset-8-gcc* 问题解决方案

1. 修改CentOS-SCLo-scl.repo

vi /etc/yum.repos.d/CentOS-SCLo-scl.repo

2. 修改此部分的baseurl

[centos-sclo-sclo]

name=CentOS-7 - SCLo sclo

baseurl=https://mirrors.aliyun.com/centos/7/sclo/x86_64/sclo/

# mirrorlist=http://mirrorlist.centos.org?arch=$basearch&release=7&repo=sclo-sclo

gpgcheck=0

enabled=1

gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-SIG-SCLo

3. 修改CentOS-SCLo-scl-rh.repo

vi /etc/yum.repos.d/CentOS-SCLo-scl-rh.repo

4. 修改此部分的baseurl

[centos-sclo-rh]

name=CentOS-7 - SCLo rh

baseurl=https://mirrors.aliyun.com/centos/7/sclo/x86_64/rh/

# mirrorlist=http://mirrorlist.centos.org?arch=$basearch&release=7&repo=sclo-rh

gpgcheck=0

enabled=1

gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-SIG-SCLo

5. 刷新缓存

yum repolist

yum clean all

yum makecache

sudo yum install -y devtoolset-8