APBS安装问题

jackie

最近需要安装g_mmpbsa程序进行binding free energy计算。在此之前需要安装Gromacs和APBS应用程序。Gromacs程序已经安装完成，目前使用是5.0.7版本。按照网页上教程所说接下来需要安装APBS1.4版本，使用如下命令：# Download using git from GitHub repository
git clone -b 1.4.1-binary-release --single-branch https://github.com/Electrostatics/apbs-pdb2pqr
cd apbs-pdb2pqr
cd apbs
cd build
sh cleanup.sh
# Installation
cmake -DCMAKE_INSTALL_PREFIX=/opt/apbs -DENABLE_BEM=off -DENABLE_iAPBS=on ..
make
sudo make install

但是，当再执行sh cleanup.sh命令的时候出现如下报错：
[root@localhost build]# sh cleanup.sh
rm: missing operand
Try 'rm --help' for more information.


于是看了一下cleanup.sh脚本文件里的内容:
[root@localhost build]# cat cleanup.sh
#!/bin/bash

rm -rf ../bin/* ../tools/bin/* ../lib/* CMakeFiles CMakeCache.txt cmake_install.cmake Makefile src install_manifest.txt apbs.cbp maloc-prefix tools fontconfig ../tests/*.pyc ../tests/io.mc ../tests/test.log doc ../doc/programmer/html ../doc/programmer/programmer.html ../doc/programmer/mainpage.h ../doc/programmer/Doxyfile ../doc/programmer/latex ../doc/programmer/programmer.pdf

find .. -name '*~' | xargs rm


发现，脚本里要删除的目录或者文件实际上有一些是不存在的，build文件夹上一级目录里的内容显示的就没有bin和lib目录等：
[root@localhost apbs]# ls
build/       BUILD.md          CMakeLists.txt  examples/       include/      README.md  test_jenkins  tools/
BUILD.html  buildWithFETK.sh  contrib/         fetk-1.5_APBS/  README.html  src/        tests/


所以我不清楚是这个脚本写的有问题还是缺少相关文件，还是我操作的问题？

于是先不理会，直接跳到下一步执行cmake命令也是出现了一些错误，如下：
[root@localhost build]# cmake -DCMAKE_INSTALL_PREFIX=/usr/local/apbs -DENABLE_BEM=off -DENABLE_iAPBS=on ..
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Setting project paths
-- Setting lookup paths for headers and libraries
-- Computing machine epsilon values
-- Floating point epsilon is 2.220446e-16
-- Double precision epsilon is 2.220446e-16
-- Looking for time
-- Looking for time - found
-- Looking for rand
-- Looking for rand - found
-- Looking for srand
-- Looking for srand - found
CMake Warning at CMakeLists.txt:231 (message):
  Did not find fetk


CMake Warning at CMakeLists.txt:242 (message):
  External maloc library was not found.


-- Looking for include file maloc/maloc.h
-- Looking for include file maloc/maloc.h - not found
CMake Warning at CMakeLists.txt:255 (message):
  External maloc headers not found.


-- Using internal contributed maloc library
-- Inline functions enabled
-- Checking for OpenMP
-- Found OpenMP_C: -fopenmp (found version "3.1")
-- Found OpenMP_CXX: -fopenmp (found version "3.1")
-- Found OpenMP: TRUE (found version "3.1")  
-- OpenMP support enabled
libs: -L/home/xiaowen/sw/apbs-pdb2pqr/apbs/build/lib -lapbs_geoflow-lmaloc-lm-fopenmp
-- Adding apbs_generic
-- With source files nosh.c;mgparm.c;femparm.c;pbeparm.c;bemparm.c;geoflowparm.c;apolparm.c;vacc.c;valist.c;vatom.c;vpbe.c;vcap.c;vclist.c;vstring.c;vparam.c;vgreen.c
-- With external header files nosh.h;mgparm.h;femparm.h;pbeparm.h;bemparm.h;geoflowparm.h;apolparm.h;vacc.h;valist.h;vatom.h;vpbe.h;vcap.h;vclist.h;vstring.h;vparam.h;vgreen.h;vmatrix.h;vhal.h;vunit.h
-- With internal header files
-- With library dependencies -L/home/xiaowen/sw/apbs-pdb2pqr/apbs/build/lib -lapbs_geoflow;-lmaloc;-lm;-fopenmp
-- Added apbs_generic
-- Adding apbs_pmgc
-- With source files buildAd.c;buildBd.c;buildGd.c;buildPd.c;cgd.c;gsd.c;matvecd.c;mgcsd.c;mgdrvd.c;mgsubd.c;mikpckd.c;mlinpckd.c;mypdec.c;newtond.c;newdrvd.c;powerd.c;smoothd.c;mgfasd.c
-- With external header files buildAd.h;buildBd.h;buildGd.h;buildPd.h;cgd.h;gsd.h;matvecd.h;mgcsd.h;mgdrvd.h;mgsubd.h;mikpckd.h;mlinpckd.h;mypdec.h;newtond.h;newdrvd.h;powerd.h;smoothd.h;mgfasd.h
-- With internal header files
-- With library dependencies -L/home/xiaowen/sw/apbs-pdb2pqr/apbs/build/lib -lapbs_geoflow;-lmaloc;-lm;-fopenmp
-- Added apbs_pmgc
-- Adding apbs_mg
-- With source files vgrid.c;vmgrid.c;vopot.c;vpmg.c;vpmgp.c
-- With external header files vgrid.h;vmgrid.h;vopot.h;vpmg.h;vpmgp.h
-- With internal header files
-- With library dependencies -L/home/xiaowen/sw/apbs-pdb2pqr/apbs/build/lib -lapbs_geoflow;-lmaloc;-lm;-fopenmp;apbs_generic;apbs_pmgc
-- Added apbs_mg
CMake Error at src/CMakeLists.txt:49 (add_subdirectory):
  add_subdirectory given source "geoflow" which is not an existing directory.


--
--  
-- -L/home/xiaowen/sw/apbs-pdb2pqr/apbs/build/lib -lapbs_geoflow;-lmaloc;-lm;-fopenmp apbs_generic;apbs_pmgc;apbs_mg
--  
-- -std=c99
-- Supplemental tools enabled
-- Building mesh
-- libraries: apbs_generic;apbs_mg;apbs_pmgc
-- Building manip
-- libraries: apbs_generic;apbs_mg;apbs_pmgc
-- Installing maloc headers
-- Building of iAPBS interface enabled
-- Configuring incomplete, errors occurred!

目前还不知道是什么原因没有解决，希望各位老师帮忙看一下，很感谢。

ene

APBS发布二进制包了啊……
https://sourceforge.net/projects/apbs/files/apbs/apbs-1.4.0/APBS-1.4-linux-static-x86_64.tar.gz/download

ene

sourceforge上还有其他1.4.x版本的二进制包，上面那个连接是1.4.0的，下载你需要的版本即可。

mjluan

ene 发表于 2019-2-18 22:50
APBS发布二进制包了啊……
https://sourceforge.net/projects/apbs/files/apbs/apbs-1.4.0/APBS-1.4-linux ...

请问这个安装包下载了之后要如何安装呢？

ene

mjluan 发表于 2019-9-2 15:30
请问这个安装包下载了之后要如何安装呢？

解压，添加环境变量就完事了。如果告诉缺库，那就缺啥补啥，下载对应的库的安装包补上。

菜菜菜

你好我现在下的这个二进制包，但是里面没有文件描述怎么添加环境变量？这不是应该有个说明什么的吗？

jackie

菜菜菜 发表于 2019-9-12 10:08
你好我现在下的这个二进制包，但是里面没有文件描述怎么添加环境变量？这不是应该有个说明什么的吗？

安装成功后确定可执行程序的安装路径，在~/.bashrc文件中source环境变量即可

tjuptz

ene 发表于 2019-9-2 17:28
解压，添加环境变量就完事了。如果告诉缺库，那就缺啥补啥，下载对应的库的安装包补上。

请教老师，我把1.5解压放进去，然后再~/.bashrc文件种加入 export PATH=$PATH:/app/apbs1.5/bin 咋把环境变量搞坏了，我后来修好了系统，是添加环境变量方式不对吗？
注：是我输错了导致的，以及遇到./apbs: error while loading shared libraries: libmaloc.so.1: cannot open shared object file: No such file or directory报错的话加上
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/app/apbs1.5/lib 加上这句就可以了

ene

tjuptz 发表于 2020-2-29 21:14
请教老师，我把1.4.2解压放进去，然后再~/.bashrc文件种加入 export PATH=$PATH:/app/APBS-1.4.2-linux64 ...

export去了

vandenberg

tjuptz 发表于 2020-2-29 21:14
请教老师，我把1.5解压放进去，然后再~/.bashrc文件种加入 export PATH=$PATH:/app/apbs1.5/bin 咋把环境 ...

我也遇到了这个问题，运行apbs提示
apbs: error while loading shared libraries: libmaloc.so.1: cannot open shared object file: No such file or directory
这个库文件实际上是存在的，在lib路径里
这是我的环境变量：
export PATH=/opt/gromacs-5.1.2/bin:$PATH
export PATH=/usr/bin/python3.5:$PATH
export PATH=/root/g_mmpbsa/bin:$PATH
export PATH=/root/APBS-1.5-linux64/bin:$PATH
export PATH=/root/APBS-1.5-linux64/lib:$PATH
请大神帮帮忙

vandenberg

vandenberg 发表于 2020-3-17 10:49
我也遇到了这个问题，运行apbs提示
apbs: error while loading shared libraries: libmaloc.so.1: canno ...

不好意思解决了
/root/APBS-1.5-linux64/lib环境变量不应该设置到PATH中，应该设置到 LD_LIBRARY_PATH中
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH/root/APBS-1.5-linux64/lib:$ LD_LIBRARY_PATH

abin

vandenberg 发表于 2020-3-17 10:49
我也遇到了这个问题，运行apbs提示
apbs: error while loading shared libraries: libmaloc.so.1: canno ...

请区分 PATH & LD_LIBRAY_PATH。

M夜J

tjuptz 发表于 2020-2-29 21:14
请教老师，我把1.5解压放进去，然后再~/.bashrc文件种加入 export PATH=$PATH:/app/apbs1.5/bin 咋把环境 ...

apbs: error while loading shared libraries: libmaloc.so.1: cannot open shared object file: No such file or directory
请问按照你说的两个路径都添加了,还是不对,还是显示这句怎么办呢?
附上我的路径export PATH=$PATH:/sob/apbs1.4.8/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/sob/apbs1.4.8/lib
感谢解答

M夜J

M夜J 发表于 2020-4-2 08:07
apbs: error while loading shared libraries: libmaloc.so.1: cannot open shared object file: No such ...

已经解决了,是因为lib文件夹里面的libmaloc.so.1 等.1文件不知道为什么都不见了,全是后缀为so.1.0.0文件了,重新下载安装了就解决了,

小土豆

vandenberg 发表于 2020-3-17 11:00
不好意思解决了
/root/APBS-1.5-linux64/lib环境变量不应该设置到PATH中，应该设置到 LD_LIBRARY_PATH中 ...

请问怎么添加环境变量呢