Previous Thread
Next Thread
Print Thread
Page 2 of 2 1 2
Re: Fortran runtime error: Bad value during integer read
sohyeon #37675 10/02/19 03:32 PM
Joined: Sep 2003
Posts: 8,485
rmv Offline
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 8,485
First, a reminder; larger, text based listings should be attached as .txt files, rather than included directly in the post. Please review the READ BEFORE POSTING topic.

Note that once you upgrade your GCC compiler suite, to run CHARMM in parallel you will probably also need to build an MPI library with the same GCC suite being used to build CHARMM, and with Fortran90 support enabled.


Rick Venable
computational chemist

Re: Fortran runtime error: Bad value during integer read
sohyeon #37728 11/26/19 03:14 AM
Joined: Aug 2019
Posts: 14
S
sohyeon Offline OP
Forum Member
OP Offline
Forum Member
S
Joined: Aug 2019
Posts: 14
I am so sorry, I forgot using the .txt files.


I set Environment Variable of gcc and cmake

export PATH=./:~/GCC-7.3.0/bin/:$PATH
export PATH=./:~/cmake-3.13.4-Linux-x86_64/bin/:$PATH


so

gcc --version : 7.7.0
cmake --version : 3.13.4

I followed "charmm/doc/cmake.info"
Configuration:: The First Step

$ mkdir charmm-build
$ ls
charmm charmm-build

From the new build directory, invoke the configure script with the desired
options.

$ cd charmm-build
$ ../charmm/configure ...
-> no occurred error in this step.


Compilation:: The Second Step
$ make -j3
-> occurred error like this..
.
.
.
[ 83%] Building Fortran object CMakeFiles/charmm_fortran.dir/lambdadyn.F90.o
[ 83%] Building Fortran object CMakeFiles/charmm_fortran.dir/rmsdyn.F90.o
[ 83%] Building Fortran object CMakeFiles/charmm_fortran.dir/replica.F90.o
[ 83%] Building Fortran object CMakeFiles/charmm_fortran.dir/umb.F90.o
[ 83%] Building Fortran object CMakeFiles/charmm_fortran.dir/secstr.F90.o
[ 83%] Building Fortran object CMakeFiles/charmm_fortran.dir/images.F90.o
[ 84%] Building Fortran object CMakeFiles/charmm_fortran.dir/upimag.F90.o
[ 84%] Building Fortran object CMakeFiles/charmm_fortran.dir/corman2.F90.o
[ 84%] Building Fortran object CMakeFiles/charmm_fortran.dir/genpsf.F90.o
[ 84%] Building Fortran object CMakeFiles/charmm_fortran.dir/cmds.F90.o
[ 84%] Building Fortran object CMakeFiles/charmm_fortran.dir/eadumb.F90.o
[ 84%] Building Fortran object CMakeFiles/charmm_fortran.dir/eval.F90.o
[ 84%] Building Fortran object CMakeFiles/charmm_fortran.dir/nbndgcm.F90.o
[ 84%] Building Fortran object CMakeFiles/charmm_fortran.dir/nbndgc.F90.o
[ 84%] Building Fortran object CMakeFiles/charmm_fortran.dir/colfft_kernel.F90.o
[ 84%] Building Fortran object CMakeFiles/charmm_fortran.dir/ancsol.F90.o
[ 84%] Building Fortran object CMakeFiles/charmm_fortran.dir/rdfsol.F90.o
/export/home/sohyeon/charmm/source/nbonds/colfft_kernel_precision.inc:475.6:
Included at /export/home/sohyeon/charmm-build/colfft_kernel.F90:111:

!$omp end atomic
1
Error: Unclassifiable OpenMP directive at (1)
/export/home/sohyeon/charmm/source/nbonds/colfft_kernel_precision.inc:475.6:
Included at /export/home/sohyeon/charmm-build/colfft_kernel.F90:117:

!$omp end atomic
1
Error: Unclassifiable OpenMP directive at (1)
make[2]: *** [CMakeFiles/charmm_fortran.dir/colfft_kernel.F90.o] error 1
make[2]: *** 끝나지 않은 작업을 기다리고 있습니다....
make[1]: *** [CMakeFiles/charmm_fortran.dir/all] error 2
make: *** [all] error 2


So I tried to again
[sohyeon@theochem11 charmm-build]$ make -j3
[ 1%] Built target qchem
[ 1%] Built target charmm_c
[ 1%] Built target charmm_cxx
[ 1%] Building Fortran object CMakeFiles/charmm_fortran.dir/primsh.F90.o
[ 1%] Building Fortran object CMakeFiles/charmm_fortran.dir/colfft_kernel.F90.o
[ 1%] Building Fortran object CMakeFiles/charmm_fortran.dir/modpsf.F90.o
/export/home/sohyeon/charmm/source/nbonds/colfft_kernel_precision.inc:475.6:
Included at /export/home/sohyeon/charmm-build/colfft_kernel.F90:111:

!$omp end atomic
1
Error: Unclassifiable OpenMP directive at (1)
/export/home/sohyeon/charmm/source/nbonds/colfft_kernel_precision.inc:475.6:
Included at /export/home/sohyeon/charmm-build/colfft_kernel.F90:117:

!$omp end atomic
1
Error: Unclassifiable OpenMP directive at (1)
make[2]: *** [CMakeFiles/charmm_fortran.dir/colfft_kernel.F90.o] error 1
make[2]: *** 끝나지 않은 작업을 기다리고 있습니다....
make[1]: *** [CMakeFiles/charmm_fortran.dir/all] error 2
make: *** [all] error 2


How do I solve it?

Last edited by sohyeon; 11/26/19 11:14 AM.
Re: Fortran runtime error: Bad value during integer read
sohyeon #37734 11/26/19 05:22 PM
Joined: Sep 2003
Posts: 8,485
rmv Offline
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 8,485
Not sure, but these version numbers in your post don't match--
Code:
export PATH=./:~/GCC-7.3.0/bin/:$PATH

gcc --version : 7.7.0

The error could be related to the compiler support for OpenMP threads, so I would probably try a different compiler. It is not an error I've seen before, but I tend to use the Intel suite more than GCC.


Rick Venable
computational chemist

Re: Fortran runtime error: Bad value during integer read
sohyeon #37737 11/27/19 01:17 AM
Joined: Aug 2019
Posts: 14
S
sohyeon Offline OP
Forum Member
OP Offline
Forum Member
S
Joined: Aug 2019
Posts: 14
I wrote it wrong.

Not gcc --version:7.7.0 but gcc--version : 7.3.0

($ gcc --version
gcc (GCC) 7.3.0
Copyright (C) 2017 Free Software Foundation, Inc.)

I will try a different complier.

Page 2 of 2 1 2

Moderated by  lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.010s Queries: 23 (0.003s) Memory: 0.9305 MB (Peak: 1.0163 MB) Data Comp: Off Server Time: 2020-08-14 10:42:13 UTC
Valid HTML 5 and Valid CSS