最新版NAMD的编译安装

退休老干部

楼主您好，我想请问一下我直接解压的binary版本，需要使用其中的ramd功能，发现README里写 “It requires NAMD to be compiled against tcl 8.3 or 8.4”,所以是需要重新编译NAMD吗？

fhh2626

退休老干部 发表于 2021-2-3 19:48
楼主您好，我想请问一下我直接解压的binary版本，需要使用其中的ramd功能，发现README里写 “It requires N ...

我没有用过，你试试编译好的MPI版本是不是可以跑

退休老干部

fhh2626 发表于 2021-2-4 10:49
我没有用过，你试试编译好的MPI版本是不是可以跑

好的，谢谢楼主

退休老干部

您好，不好意思打扰了，我想请问一下关于NAMD版本编译的问题。现在我想比较不同核数（8核，16核，32核）并行的运行速度，一个队列有16个核，如果测试32个核的话，就需要分节点了，所以我应该编译哪个版本啊，我尝试编译verbs-linux-x86_64  smp，发现build的时候就出现这样的问题了：
In file included from cpuaffinity.C:28:0:
/usr/include/infiniband/verbs.h: In function ‘verbs_context* verbs_get_ctx(const ibv_context*)’:
/usr/include/infiniband/verbs.h:924:10: error: cannot convert ‘ibv_context’ to ‘const int’ in initialization
   NULL : container_of(ctx, struct verbs_context, context);
          ^
/usr/include/infiniband/verbs.h:924:10: error: expected ‘,’ or ‘;’ before ‘*’ token
   NULL : container_of(ctx, struct verbs_context, context);
          ^
/usr/include/infiniband/verbs.h:924:10: error: ‘__mptr’ was not declared in this scope
   NULL : container_of(ctx, struct verbs_context, context);
          ^
/usr/include/infiniband/verbs.h:923:62: error: third operand to the conditional operator is of type ‘void’, but the second operand is neither a throw-expression nor of type ‘void’
  return (!ctx || (ctx->abi_compat != ((uint8_t *)NULL) - 1)) ?
                                                              ^
/usr/include/infiniband/verbs.h: In function ‘verbs_device* verbs_get_device(const ibv_device*)’:
/usr/include/infiniband/verbs.h:931:10: error: cannot convert ‘ibv_device’ to ‘const int’ in initialization
   NULL : container_of(dev, struct verbs_device, device);
          ^
/usr/include/infiniband/verbs.h:931:10: error: expected ‘,’ or ‘;’ before ‘*’ token
   NULL : container_of(dev, struct verbs_device, device);
          ^
/usr/include/infiniband/verbs.h:931:10: error: ‘__mptr’ was not declared in this scope
   NULL : container_of(dev, struct verbs_device, device);
          ^
/usr/include/infiniband/verbs.h:930:34: error: third operand to the conditional operator is of type ‘void’, but the second operand is neither a throw-expression nor of type ‘void’
  return (dev->ops.alloc_context) ?
                                  ^
Fatal Error by charmc in directory /gpfs01/home/xiafei2/yqwang/software/NAMD_2.14_Source/charm-6.10.2/verbs-linux-x86_64-smp/tmp
   Command g++ -DCMK_GFORTRAN -D_REENTRANT -I../bin/../include -D__CHARMC__=1 -I. -O3 -U_FORTIFY_SOURCE -fno-stack-protector -std=c++11 -fno-lifetime-dse -c cpuaffinity.C -o cpuaffinity.o returned error code 1
charmc exiting...
gmake: *** [cpuaffinity.o] Error 1
-------------------------------------------------
Charm++ NOT BUILT. Either cd into verbs-linux-x86_64-smp/tmp and try
to resolve the problems yourself, visit
http://charm.cs.illinois.edu/
for more information. Otherwise, email the developers at charm@cs.illinois.edu

请问这是什么原因？

fhh2626

退休老干部 发表于 2021-2-27 13:18
您好，不好意思打扰了，我想请问一下关于NAMD版本编译的问题。现在我想比较不同核数（8核，16核，32核）并 ...

如果你只想在当前节点运行的话就编译multicore版本，如果你有infiniband的话就编译跨节点infiniband版本

退休老干部

fhh2626 发表于 2021-2-27 15:56
如果你只想在当前节点运行的话就编译multicore版本，如果你有infiniband的话就编译跨节点infiniband版本

好的，谢谢。我还想请问一下跨节点跟SMP没有关系吗？

fhh2626

退休老干部 发表于 2021-2-27 16:16
好的，谢谢。我还想请问一下跨节点跟SMP没有关系吗？

没关系

957

求问按照以上安装NAMD2.13 最后一步make 出现以下error
src/colvarproxy_namd.C: In member function ‘virtual int colvarproxy_namd::setup()’:
src/colvarproxy_namd.C:252: error: ‘modifyGridObjForces’ was not declared in this scope
src/colvarproxy_namd.C: In member function ‘virtual int colvarproxy_namd::reset()’:
src/colvarproxy_namd.C:269: error: ‘modifyRequestedGridObjects’ was not declared in this scope
src/colvarproxy_namd.C: In member function ‘virtual void colvarproxy_namd::calculate()’:
src/colvarproxy_namd.C:468: error: ‘getGridObjIndexBegin’ was not declared in this scope
src/colvarproxy_namd.C:469: error: ‘getGridObjValueBegin’ was not declared in this scope
src/colvarproxy_namd.C:470: error: ‘getGridObjValueEnd’ was not declared in this scope
src/colvarproxy_namd.C:540: error: ‘modifyGridObjForces’ was not declared in this scope
src/colvarproxy_namd.C:540: error: ‘requestedGridObjs’ was not declared in this scope
src/colvarproxy_namd.C:542: error: ‘getGridObjIndexBegin’ was not declared in this scope
src/colvarproxy_namd.C:544: error: ‘getGridObjIndexEnd’ was not declared in this scope
src/colvarproxy_namd.C: In member function ‘virtual int colvarproxy_namd::init_volmap_by_id(int)’:
src/colvarproxy_namd.C:1215: error: ‘modifyRequestedGridObjects’ was not declared in this scope
src/colvarproxy_namd.C: In member function ‘virtual int colvarproxy_namd::init_volmap_by_name(const char*)’:
src/colvarproxy_namd.C:1257: error: ‘modifyRequestedGridObjects’ was not declared in this scope
make: *** [obj/colvarproxy_namd.o] Error 1
这要怎么处理呢

fhh2626

957 发表于 2021-5-25 15:46
求问按照以上安装NAMD2.13 最后一步make 出现以下error
src/colvarproxy_namd.C: In member function ‘vi ...

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
make -jxxx

957

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

按照您说的执行了一次，还是一样的错误

fhh2626

957 发表于 2021-5-25 16:04
按照您说的执行了一次，还是一样的错误

你执行make depends有什么输出吗

957

fhh2626 发表于 2021-5-25 16:46
你执行make depends有什么输出吗

有的
checking dependencies for colvars/src/colvarparse.cpp
checking dependencies for colvars/src/colvarproxy.cpp
checking dependencies for colvars/src/colvarproxy_volmaps.cpp
checking dependencies for colvars/src/colvarproxy_replicas.cpp
checking dependencies for colvars/src/colvarproxy_tcl.cpp
checking dependencies for colvars/src/colvarscript.cpp
checking dependencies for colvars/src/colvarscript_commands.cpp
checking dependencies for colvars/src/colvarscript_commands_bias.cpp
checking dependencies for colvars/src/colvarscript_commands_colvar.cpp
checking dependencies for colvars/src/colvartypes.cpp
checking dependencies for colvars/src/colvarvalue.cpp
checking dependencies for colvars/src/nr_jacobi.cpp
checking dependencies for lepton/src/CompiledExpression.cpp
checking dependencies for lepton/src/ExpressionProgram.cpp
checking dependencies for lepton/src/ExpressionTreeNode.cpp
checking dependencies for lepton/src/Operation.cpp
checking dependencies for lepton/src/ParsedExpression.cpp
checking dependencies for lepton/src/Parser.cpp
类似于这样

fhh2626

957 发表于 2021-5-26 11:29
有的
checking dependencies for colvars/src/colvarparse.cpp
checking dependencies for colvars/src ...

实在不行你就下编译好的版本吧，NAMD2.13实在太老了，不知道有什么兼容性问题

azero

奇怪，在旧笔记本是可以成功编译的

新笔记本出现了fftw的问题

can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: .rootdir/fftw/lib/libsfftw.a(wisdomio.o): relocation R_X86_64_32 against `.text' can no
t be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: .rootdir/fftw/lib/libsfftw.a(putils.o): relocation R_X86_64_32S against `.rodata' can n
ot be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: .rootdir/fftw/lib/libsfftw.a(rader.o): relocation R_X86_64_32 against symbol `fftw_twid
dle_rader' can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: .rootdir/fftw/lib/libsfftw.a(twiddle.o): relocation R_X86_64_32 against `.bss' can not
be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: .rootdir/fftw/lib/libsrfftw.a(rexec2.o): warning: relocation in read-only section `.eh_
frame'
collect2: error: ld returned 1 exit status


解决不了，NAMDlib.zip 已经解压放进文件夹

fhh2626

azero 发表于 2021-6-16 16:19
奇怪，在旧笔记本是可以成功编译的

新笔记本出现了fftw的问题

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adding the option -no-pie to CXXOPTS in the relevant arch file (eg. Linux-x86_64-g++.arch)