最新版NAMD的编译安装

azero · 发表于 Post on 2021-6-17 13:24:03

fhh2626 发表于 2021-6-17 10:10
ubuntu维护者在默认的gcc编译器里面加了一堆乱七八糟的选项，用默认的编译器容易出问题

这个错误需要a ...

谢谢，按照楼主的做法试了试
最后两行是charmc: Executing rm -f charmrun
rm -f moduleinit8279.C moduleinit8279.o
应该是安装成功了

不过中途有文字
OpenMP support not enabled
应该不影响吧，笔记本装了openmpi的

penMP support not enabled

d2denis · 发表于 Post on 2021-8-26 10:06:19

NAMD_2.14_Source/Linux-x86_64-g++$ make -j24
Makefile:432: .rootdir/Plumed.inc: No such file or directory
make: *** No rule to make target '.rootdir/Plumed.inc'. Stop.
请问必须要是有了PLUMED才能装的吗?

fhh2626 · 发表于 Post on 2021-8-26 10:15:30

d2denis 发表于 2021-8-26 10:06
NAMD_2.14_Source/Linux-x86_64-g++$ make -j24
Makefile:432: .rootdir/Plumed.inc: No such file or dir ...

没见过这个错误，你是怎么操作的？

d2denis · 发表于 Post on 2021-8-26 10:42:19

本帖最后由 d2denis 于 2021-8-26 10:58 编辑

fhh2626 发表于 2021-8-26 10:15
没见过这个错误，你是怎么操作的？

基本按照您给的步骤走的,不过两个版本都是最新的:
NAMD_2.14_Source和charm-6.10.2
补充
....
是我忘了已经用plumed patch了,换了个新的电脑问题已经解决了,谢谢大佬

刘金磊 · 发表于 Post on 2021-12-7 11:15:49

有谁知道这是怎么回事？

jcm · 发表于 Post on 2021-12-9 09:54:48

sophie940122 发表于 2019-11-19 09:32
**** 作者被禁止或删除内容自动屏蔽 ****

我也是这个问题

tjuptz · 发表于 Post on 2022-4-3 17:17:55

fhh2626 发表于 2021-5-25 15:52
先把Linux-x86_64-g++/文件夹删了
重新config一次，然后进入Linux-x86_64-g++/文件夹
make depends

fu老师您好，我在编译NAMD2.12CUDA版时也是遇到了类似38#的问题，用您说的这个也是不行。
因为想用文献里一个2.12带磁场补丁包的版本，所以用的这个老版本。CPU版本编译没问题，现在试试GPU版遇到了上述问题。您还有其他建议吗？

In file included from src/CudaPmeSolverUtil.C:9:0:
src/CudaPmeSolverUtil.C: In member function ‘virtual void CudaFFTCompute::plan3D(int*, int)’:
src/CudaPmeSolverUtil.C:51:85: error: ‘cufftSetCompatibilityMode’ was not declared in this scope
cufftCheck(cufftSetCompatibilityMode(forwardPlan, CUFFT_COMPATIBILITY_FFTW_PADDING));
^
src/CudaPmeSolverUtil.h:18:21: note: in definition of macro ‘cufftCheck’
cufftResult err = stmt; \
^
src/CudaPmeSolverUtil.C:52:86: error: ‘cufftSetCompatibilityMode’ was not declared in this scope
cufftCheck(cufftSetCompatibilityMode(backwardPlan, CUFFT_COMPATIBILITY_FFTW_PADDING));
^
src/CudaPmeSolverUtil.h:18:21: note: in definition of macro ‘cufftCheck’
cufftResult err = stmt; \
^
src/CudaPmeSolverUtil.C: In member function ‘virtual void CudaFFTCompute::plan2D(int*, int, int)’:
src/CudaPmeSolverUtil.C:64:85: error: ‘cufftSetCompatibilityMode’ was not declared in this scope
cufftCheck(cufftSetCompatibilityMode(forwardPlan, CUFFT_COMPATIBILITY_FFTW_PADDING));
^
src/CudaPmeSolverUtil.h:18:21: note: in definition of macro ‘cufftCheck’
cufftResult err = stmt; \
^
src/CudaPmeSolverUtil.C:65:86: error: ‘cufftSetCompatibilityMode’ was not declared in this scope
cufftCheck(cufftSetCompatibilityMode(backwardPlan, CUFFT_COMPATIBILITY_FFTW_PADDING));
^
src/CudaPmeSolverUtil.h:18:21: note: in definition of macro ‘cufftCheck’
cufftResult err = stmt; \
^
src/CudaPmeSolverUtil.C: In member function ‘virtual void CudaFFTCompute::plan1DX(int*, int, int)’:
src/CudaPmeSolverUtil.C:76:85: error: ‘cufftSetCompatibilityMode’ was not declared in this scope
cufftCheck(cufftSetCompatibilityMode(forwardPlan, CUFFT_COMPATIBILITY_FFTW_PADDING));
^
src/CudaPmeSolverUtil.h:18:21: note: in definition of macro ‘cufftCheck’
cufftResult err = stmt; \
^
src/CudaPmeSolverUtil.C:77:86: error: ‘cufftSetCompatibilityMode’ was not declared in this scope
cufftCheck(cufftSetCompatibilityMode(backwardPlan, CUFFT_COMPATIBILITY_FFTW_PADDING));
^
src/CudaPmeSolverUtil.h:18:21: note: in definition of macro ‘cufftCheck’
cufftResult err = stmt; \
^
src/CudaPmeSolverUtil.C: In member function ‘virtual void CudaFFTCompute::plan1DY(int*, int, int)’:
src/CudaPmeSolverUtil.C:88:85: error: ‘cufftSetCompatibilityMode’ was not declared in this scope
cufftCheck(cufftSetCompatibilityMode(forwardPlan, CUFFT_COMPATIBILITY_FFTW_PADDING));
^
src/CudaPmeSolverUtil.h:18:21: note: in definition of macro ‘cufftCheck’
cufftResult err = stmt; \
^
src/CudaPmeSolverUtil.C:89:86: error: ‘cufftSetCompatibilityMode’ was not declared in this scope
cufftCheck(cufftSetCompatibilityMode(backwardPlan, CUFFT_COMPATIBILITY_FFTW_PADDING));
^
src/CudaPmeSolverUtil.h:18:21: note: in definition of macro ‘cufftCheck’
cufftResult err = stmt; \
^
In file included from inc/ComputePmeCUDAMgr.decl.h:7:0,
from src/ComputePmeCUDAMgr.h:9,
from src/CudaPmeSolver.C:5:
inc/CudaPmeSolver.decl.h:1258:35: warning: ‘auto_ptr’ is deprecated (declared at /usr/include/c++/4.8.2/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
std::auto_ptr<SDAG::Dependency> __dep; \
^
src/CudaPmeSolver.h:86:2: note: in expansion of macro ‘CudaPmePencilXY_SDAG_CODE’
CudaPmePencilXY_SDAG_CODE
^
src/CudaPmeSolverUtil.C: In member function ‘virtual void CudaFFTCompute::plan1DZ(int*, int, int)’:
src/CudaPmeSolverUtil.C:100:85: error: ‘cufftSetCompatibilityMode’ was not declared in this scope
cufftCheck(cufftSetCompatibilityMode(forwardPlan, CUFFT_COMPATIBILITY_FFTW_PADDING));
^
src/CudaPmeSolverUtil.h:18:21: note: in definition of macro ‘cufftCheck’
cufftResult err = stmt; \
^
src/CudaPmeSolverUtil.C:101:86: error: ‘cufftSetCompatibilityMode’ was not declared in this scope
cufftCheck(cufftSetCompatibilityMode(backwardPlan, CUFFT_COMPATIBILITY_FFTW_PADDING));
^
src/CudaPmeSolverUtil.h:18:21: note: in definition of macro ‘cufftCheck’
cufftResult err = stmt; \
^
inc/CudaPmeSolver.decl.h:1911:35: warning: ‘auto_ptr’ is deprecated (declared at /usr/include/c++/4.8.2/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
std::auto_ptr<SDAG::Dependency> __dep; \
^
src/CudaPmeSolver.h:114:2: note: in expansion of macro ‘CudaPmePencilX_SDAG_CODE’
CudaPmePencilX_SDAG_CODE
^
inc/CudaPmeSolver.decl.h:2715:35: warning: ‘auto_ptr’ is deprecated (declared at /usr/include/c++/4.8.2/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
std::auto_ptr<SDAG::Dependency> __dep; \
^
src/CudaPmeSolver.h:142:2: note: in expansion of macro ‘CudaPmePencilY_SDAG_CODE’
CudaPmePencilY_SDAG_CODE
^
inc/CudaPmeSolver.decl.h:3517:35: warning: ‘auto_ptr’ is deprecated (declared at /usr/include/c++/4.8.2/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
std::auto_ptr<SDAG::Dependency> __dep; \
^
src/CudaPmeSolver.h:177:2: note: in expansion of macro ‘CudaPmePencilZ_SDAG_CODE’
CudaPmePencilZ_SDAG_CODE
^
g++ -m64 -std=c++0x -O3 -I/app/NAMD_2.12_Source/charm-6.7.1/include -DCMK_OPTIMIZE=1 -Isrc -Iinc -Iplugins/include -DSTATIC_PLUGIN -I.rootdir/tcl/include -DNAMD_TCL -I.rootdir/fftw/include -DNAMD_FFTW -DNAMD_CUDA -I. -I/usr/local/cuda/include -I.rootdir/cub -DNAMD_VERSION="2.12" -DNAMD_PLATFORM="Linux-x86_64-multicore-CUDA" -DREMOVE_PROXYRESULTMSG_EXTRACOPY -DNODEAWARE_PROXY_SPANNINGTREE -DUSE_NODEPATCHMGR -DUSE_CKLOOP=1 -fexpensive-optimizations -ffast-math -o obj/DumpBench.o -c src/DumpBench.C
make: *** [obj/CudaPmeSolverUtil.o] Error 1
make: *** Waiting for unfinished jobs....

复制代码

fhh2626 · 发表于 Post on 2022-4-5 11:08:29

tjuptz 发表于 2022-4-3 17:17
fu老师您好，我在编译NAMD2.12CUDA版时也是遇到了类似38#的问题，用您说的这个也是不行。
因为想用文献 ...

你试试用gcc7或者gcc8编译呢？

tjuptz · 发表于 Post on 2022-4-5 20:01:42

本帖最后由 tjuptz 于 2022-4-5 21:05 编辑

fhh2626 发表于 2022-4-5 11:08
你试试用gcc7或者gcc8编译呢？

换用gcc7和gcc8试了一下，还是同样的模块出问题@_@

fhh2626 · 发表于 Post on 2022-4-6 10:39:54

tjuptz 发表于 2022-4-5 20:01
换用gcc7和gcc8试了一下，还是同样的模块出问题@_@

也许是你的GPU太新了，NAMD2.12不支持吧

tjuptz · 发表于 Post on 2022-4-6 11:06:32

fhh2626 发表于 2022-4-6 10:39
也许是你的GPU太新了，NAMD2.12不支持吧

硬件rtx2060，cuda10.2。可能是，毕竟版本有点老了。总之，谢谢fu老师解答。

wangke · 发表于 Post on 2022-8-2 15:54:52

各位老师好，我在运行namd3上遇到了一些小问题，我使用的namd3是从源码编译的UCX-SMP版本，编译在超算上，
运行的命令是：/HOME/scz3470/run/namd/Linux-x86_64-g++/charmrun +p16 /HOME/scz3470/run/namd/Linux-x86_64-g++/namd3 +ignoresharing +isomalloc_sync +devices 0,1 +replicas 16 fep_${system}.conf --source FEP_remd_relative.namd +stdout output_${system}/%d/job${cnt}.%d.log
我得到的反馈结果是：
FATAL ERROR: ComputeCUDAMgr::createCudaComputeNonbonded, non-bonded CUDA tables not created
FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
然后我查了一下，我搜索到了，如下结果：

有老师可以指点一下吗，不胜感激。

fygfjhj · 发表于 Post on 2023-6-5 16:11:11

楼主是从源码编译吗，我下载二进制包可以直接使用namd程序，想问下您这样安装和使用二进制包的效果是一样的吗

fhh2626 · 发表于 Post on 2023-6-5 16:58:39

fygfjhj 发表于 2023-6-5 16:11
楼主是从源码编译吗，我下载二进制包可以直接使用namd程序，想问下您这样安装和使用二进制包的效果是一样的 ...

一般情况下是一样的

Amphibiouskii · 发表于 Post on 2023-7-7 10:59:06

更新NAMD中的Colvars，注意编译Colvars还需要OpenMM中的Lepton
export OPENMM_SOURCE=xxxxxxxxxxxxxxxxxxx
sh ./colvars-master/update-colvars-code.sh ./NAMD_Git-2018-08-23_Source

请问老师这一部分是需要自己先安装OpenMM的意思吗？如果我直接执行那个sh，会得到下面这样的输出：

Detected NAMD source tree in ./NAMD_Git-2022-07-21_Source
Updating ...Downloading Lepton library (used in Colvars) via the OpenMM repository
Cloning into '/tmp/openmm-source-RRGVgo'...
remote: Enumerating objects: 2119, done.
remote: Counting objects: 100% (2119/2119), done.
remote: Compressing objects: 100% (1571/1571), done.
remote: Total 2119 (delta 865), reused 1182 (delta 492), pack-reused 0
Receiving objects: 100% (2119/2119), 18.31 MiB | 1.08 MiB/s, done.
Resolving deltas: 100% (865/865), done.
.../colvars-master/update-colvars-code.sh: line 367: namd/Makefile.patch: No such file or directory
...................................................................................... done.
*************************************************
Please run "make depends" in the NAMD tree.
*************************************************

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之后make depends则会报错：

Make.depends:7787: .rootdir/lepton/Make.depends: No such file or directory
make: *** No rule to make target '.rootdir/lepton/Make.depends'. Stop.

复制代码

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[NAMD] 最新版NAMD的编译安装