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#37273 - 01/12/19 04:45 AM Installation error
Rohit Offline
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Registered: 10/25/17
Posts: 33
Loc: Hyderabad, India
I am installing 42b1 of charmm

tried ./install.com gnu M

HARMM Build on gnu Sat Jan 12 15:09:09 IST 2019
Sat Jan 12 15:09:09 IST 2019
Makefile:25: *** AVX-compatible CPU requires gcc version >= 4.6.0 for CHARMM compilation. Stop

tried ./install.com em64t M

CHARMM Build on em64t Sat Jan 12 15:08:38 IST 2019

/home/flab/Documents/charmm/tool/preflx /home/flab/Documents/charmm/source/ltm/aaa_sanity_checks.src
aaa_sanity_checks.src: /usr/bin/g++/prefx_em64t: Not a directory.
cat: prefx.msg: No such file or directory
ltm.mk:21: recipe for target 'aaa_sanity_checks.o' failed
make: *** [aaa_sanity_checks.o] Error 1

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#37275 - 01/12/19 12:09 PM Re: Installation error [Re: Rohit]
rmv Online   content

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Registered: 09/17/03
Posts: 8314
Loc: 39 03 48 N, 77 06 54 W
The GCC issue is a bug, fixed in more recent versions. The fix is in build/UNX/Makefile_gnu

Code:
16c16
< GCC_GTEQ_460 := $(shell expr `gcc -dumpversion` \>= 4.6)
---
> GCC_GTEQ_460 := $(shell expr `gcc -dumpversion | sed -e 's/\.\([0-9][0-9]\)/\1/g' -e 's/\.\([0-9]\)/0\1/g' -e 's/^[0-9]\{3,4\}$$/&00/'` \>= 40600)

The corrected version is the first line in the code snippet above.

The Intel compiler must be installed and available in the command search path for the Linux shell in order to use the em64t option. One of the first steps is build a custom source code pre-processor, prefx_em64t, which should be created in the 'tool' subdir of the charmm root directory.

You could also try the alternate installation procedure; see cmake.doc




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Rick Venable
computational chemist


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#37278 - 01/14/19 07:41 AM Re: Installation error [Re: Rohit]
Rohit Offline
Forum Member

Registered: 10/25/17
Posts: 33
Loc: Hyderabad, India
using ./install.com gnu M gives error as follows in log

f951: Fatal Error: Reading module Ďallocationí at line 1592 column 65: Unexpected EOF
compilation terminated.
memory.mk:42: recipe for target 'realloc_mod.o' failed
make: *** [realloc_mod.o] Error 1

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#37279 - 01/14/19 10:51 AM Re: Installation error [Re: Rohit]
rmv Online   content

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Registered: 09/17/03
Posts: 8314
Loc: 39 03 48 N, 77 06 54 W
That's not a problem I've seen before, and I have done some 'gnu' builds recently.

What are the OS and compiler versions?

I often try a non-parallel build first, to test the compiler setup w/o any additional libraries (e.g. MPI).

Make sure to clean up from previous builds; I usually do

rm -rf lib/gnu build/gnu
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Rick Venable
computational chemist


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#37280 - 01/14/19 11:10 PM Re: Installation error [Re: Rohit]
Rohit Offline
Forum Member

Registered: 10/25/17
Posts: 33
Loc: Hyderabad, India
when used dpkg --list | grep compiler below is the output of list of compilers.
OS - ubuntu 18.04

flab@PT-3620:~/Documents/charmm$ dpkg --list | grep compiler
ii g++ 4:7.3.0-3ubuntu2.1 amd64 GNU C++ compiler
ii g++-7 7.3.0-27ubuntu1~18.04 amd64 GNU C++ compiler
ii gcc 4:7.3.0-3ubuntu2.1 amd64 GNU C compiler
ii gcc-7 7.3.0-27ubuntu1~18.04 amd64 GNU C compiler
ii gfortran 4:7.3.0-3ubuntu2.1 amd64 GNU Fortran 95 compiler
ii gfortran-7 7.3.0-27ubuntu1~18.04 amd64 GNU Fortran compiler
ii libllvm6.0:amd64 1:6.0-1ubuntu2 amd64 Modular compiler and toolchain technologies, runtime library
ii libllvm6.0:i386 1:6.0-1ubuntu2 i386 Modular compiler and toolchain technologies, runtime library
ii libparams-validationcompiler-perl 0.26-1 all module to build an optimized subroutine parameter validator
ii libxkbcommon0:amd64 0.8.0-1ubuntu0.1 amd64 library interface to the XKB compiler - shared library

rm -rf lib/gnu build/gnu tried to reinstall but still same error.

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#37281 - 01/15/19 12:19 PM Re: Installation error [Re: Rohit]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8314
Loc: 39 03 48 N, 77 06 54 W
Which compiler(s) are being used to compile CHARMM?
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Rick Venable
computational chemist


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#37282 - 01/15/19 06:18 PM Re: Installation error [Re: Rohit]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8314
Loc: 39 03 48 N, 77 06 54 W
Using c42b1 with the change to build/UNX/Makefile_gnu noted above, I was able to build CHARMM using the GCC 7.3 suite on Ubuntu 18.04 without MPI via

./install.com gnu

(Our cluster nodes use CentOS, so we do our MPI builds on CentOS machines.)
_________________________
Rick Venable
computational chemist


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#37289 - 01/17/19 09:14 AM Re: Installation error [Re: Rohit]
Rohit Offline
Forum Member

Registered: 10/25/17
Posts: 33
Loc: Hyderabad, India
How can i specify installer to use specific compiler?

I am using gnu, Not sure. is there a way to specify compiler for charmm installation.

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#37290 - 01/17/19 11:48 AM Re: Installation error [Re: Rohit]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8314
Loc: 39 03 48 N, 77 06 54 W
The log file (e.g. build/gnu_M/gnu.log) may confirm which compiler was used. You can also use the following commands to get filesystem location and versions for the compilers via

# get full path names
which gcc
which gfortran
# get version info
gcc --version
gfortran --version

The versions should be identical, and the path names typically begin with /usr/bin.

The install.com script expects the user to set up the compile time environment beforehand; how that is done depends on how the hosts in your workgroup are being managed. In general, to override the default compilers, the environment variables PATH and LD_LIBRARY_PATH will need to be changed.

For parallel usage with an MPI implementation, the commands mpif90 and mpicc also need to be available (try 'which' again), along with an file named mpi.mod that was built with Fortran90 support using the same GCC version that will be used to compile CHARMM. The PATH and LD_LIBRARY_PATH environment variables may need further changes for MPI builds. We use modules to manage the use of compilers and added libraries on our clustet and desktop systems, but for an isolated host, you may have to learn how to do this for yourself.



Edited by rmv (01/17/19 04:18 PM)
Edit Reason: corrected log file name
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computational chemist


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