在linux系统下怎么安装amber tools20呢？

abin

AmberTools 是免费的。
Amber核心，是付费的。

sobereva

sharslve 发表于 2021-6-27 21:40
你好，请问有amber的安装包吗？我申请了但是没申请下来。

Amber本来就不是能免费申请的
分清楚Amber和AmberTools

sharslve

sobereva 发表于 2021-7-1 05:41
Amber本来就不是能免费申请的
分清楚Amber和AmberTools

谢谢回复，我已经申请到Amber20了，中国的可以发邮件免费申请，就是时间比较久，申请到批准到发下载地址总共花了两个星期左右。

scfslyzkf

hhhnano 发表于 2020-6-18 11:59
Amber20和以前版本安装有很大差别，且自动生成安装目录amber20,安装文件采用cmake_run文件安装，每部安装要 ...

官方的教程，步骤看上去很简单，但是编译起来经常出错，也没有给出相应环境变量配置的详细解释。
从miniconda装二进制版相对简单的多，但是不能并行，也是一个问题。

494085639

hhhnano 发表于 2020-6-18 11:59
Amber20和以前版本安装有很大差别，且自动生成安装目录amber20,安装文件采用cmake_run文件安装，每部安装要 ...

你好想问下在哪里可以下载到两个压缩包?

snljty

494085639 发表于 2021-11-25 09:16
你好想问下在哪里可以下载到两个压缩包?

AmberTools21官网直接能下。Amber20现在对北美西欧霓虹以外的地方学术机构开源免费，但是需要自己去发邮件申请。申请方式自己看官网。

聂佳伟

新人不能去下载网址下载

sobereva

聂佳伟 发表于 2021-12-3 22:37
新人不能去下载网址下载

不可能不能下
不能下说清楚怎么不能下

azero

hhhnano 发表于 2020-6-18 11:59
Amber20和以前版本安装有很大差别，且自动生成安装目录amber20,安装文件采用cmake_run文件安装，每部安装要 ...

解压文件夹名称是amber20_src，安装在amber文件夹，
安装完能删掉amber20_src文件夹么，
export AMBERHOME=/home/user/amber2020/amber20_src 这句搞得不敢删掉amber20_src文件夹

这文件夹挺大的

uenh1998

我是在./run cmake阶段出现了这样的错误，请问该怎么处理呢？
Could NOT find Readline (missing: READLINE_INCLUDE_DIR READLINE_LIBRARY READLINE_WORKS)
CMake Error at cmake/3rdPartyTools.cmake:84 (message):
  3rd party program readline is not bundled and cannot be built inside Amber.
Call Stack (most recent call first):
  cmake/3rdPartyTools.cmake:189 (set_3rdparty)
  CMakeLists.txt:190 (include)


-- Configuring incomplete, errors occurred!
See also "/nh/amber20_src/build/CMakeFiles/CMakeOutput.log".
See also "/nh/amber20_src/build/CMakeFiles/CMakeError.log".

If the cmake build report looks OK, you should now do the following:

    make install
    source /nh/amber20/amber.sh

Consider adding the last line to your login startup script, e.g. ~/.bashrc

Santz

uenh1998 发表于 2022-2-21 12:55
我是在./run cmake阶段出现了这样的错误，请问该怎么处理呢？
Could NOT find Readline (missing: READLIN ...

sudo yum install readline readline-devel -y

robert2005

hhhnano 发表于 2020-6-18 11:59
Amber20和以前版本安装有很大差别，且自动生成安装目录amber20,安装文件采用cmake_run文件安装，每部安装要 ...

export AMBERHOME=/home/user/amber2020/amber20_src

一、串行安装
cd amber20_src/build
# optional: edit the run_cmake script to make any needed changes;
# most users should not need to do this
./run_cmake
# Next, build and install the code:
make install

source /home/xzhfood/amber2020/amber20/amber.sh

cd $AMBERHOME
make test.serial
第一行export路径是不是错了啊，我看最后cd $AMBERHOME不是第一行export的路径啊？

robert2005

按照手册装貌似并行总是失败啊，无法安装并行版啊？哪位大神并行版安装成功了啊？

robert2005

二、并行安装
#compile the parallel (MPI)

cd $AMBERHOME/AmberTools/src
./configure_mpich gnu
这个里面的$AMBERHOME/AmberTools/src这个路径到底是哪个目录啊？
amber20/AmberTools/src???
amber20_src/AmberTools/src???

robert2005

看这个安装过程感觉有些疑惑，$AMBERHOME到底是指哪个路径啊？感觉一会是amber20_src/AmberTools/src???
后来又变成了amber20/AmberTools/src???
或者说安装之前的export是不必要的，不用定义，安装后程序自动定义为amber20/AmberTools/src???
但是这样的话，后期并行就怎么都无法安装成功。
另外还有就是把openmpi或mpich解压到哪个路径啊？
amber20/AmberTools/src???
amber20_src/AmberTools/src???
解压后是个什么形式？比如
amber20_src/AmberTools/src/openmpi???
官网网页上说
Some programs in Amber (e.g., pmemd, cpptraj, etc.) can be built and installed in their parallel MPI version. If you want to build and install these MPI programs, you will need to provide a MPI compiler like OpenMPI or MPICH. The OpenMPI and MPICH system installations provided by CentOS (i.e., through yum install) are known to be somehow incompatible with Amber20.

One recommendation is to download a recent version of OpenMPI at open-mpi.org, untar the distribution in amber20_src/AmberTools/src, and execute in that directory the configure_openmpi script. (Do this after you have done a serial install, and have sourced the amber.sh script in the installation folder to create an AMBERHOME environment variable.) Similar instructions apply to MPICH, (see mpich.org,) but at least one user has reported configuration problems with this on CentOS7.
是amber20_src/AmberTools/src
手册上说
cd $AMBERHOME/AmberTools/src
./configure_mpich <compiler>
但是装完串行后，$AMBERHOME已经是amber20了，不是amber20_src了啊？
这个是不是有点矛盾啊？
我在centos7和8上装了好几遍了，串行都还好，并行版都是一样的错误：
error: Cannot link MPI programs. Check your configuration!!!
哪位大佬知道什么原因吗？