AMBER Archive (2007)

Subject: RE: Re: AMBER: on PATH

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Thu Jun 28 2007 - 12:12:43 CDT

Dear Ross:
Thanks. make (serial) exited with errors aboul leap.

--- Ross Walker <ross_at_rosswalker.co.uk> wrote:

> Hi Francesco,
>
> > ./configure -static ifort_x86_64
> > ./configure: line 1264: config.h: Permission denied
>
> The issue is one of Unix file permissions. I suspect that you don't own the
> amber9 directory and all sub files. You have one of two options, either
> chown the directory to yourself and then repeat the installation or do the
> installation as root - which you tried...
>
> If you run the installation as root you have to make sure that root picks up
> all the environment variables etc.

Particularly with my system. being the only user, I tend to put as much as
possible into my .bashrc.

>Thus it is probably easier to just chown
> everything to you.
>
> su -
> cd /path_to_amber9/
> cd ../
> chown -R username amber9 (where username is your username)
> exit (quits as root and should be back as your
> user)

Other than chown, also run

chgrp -R username amber9

>
> cd $AMBERHOME/src/

I removed previous config.h

> ./configure -static ifort_x86_64

This created new config.h

> make clean

> make

After a long session it exited with Error 2

Those errors that I can see on the screen comprise:

WcActCB.c:1448: error: expected declaration specifiers before XEvent.

WcActCB.c:1448: error: expected declaration specifiers before Cardinal.

WcActCB.c: In function WcDynamicActionACT:

WcActCB.c:1450: error: expected declaration specifiers before Widget.

WcActCB.c:1450: error: expected declaration specifiers before XEvent.

WcActCB.c:1450: error: expected declaration specifiers before Cardinal.

WcActBC.c: In function WcDynamicCallbackACT:

WcActCB.c:1452: error: expected declaration specifiers before Widget.

WcActCB.c:1452: error: expected declaration specifiers before XEvent.

WcActCB.c:1452: error: expected declaration specifiers before Cardinal.

WcActBC.c: In function WcRegisterWcActions:

WcActCB.c:1461: error: expected declaration specifiers before XtAppContext.

WcActCB.c:1463: error: expected = , , , ;, asm or __attribute__ befor WcActions

WcActCB.c:1463 error: WcActions undeclared (first use in this function).

WcActCB.c:1463 error: expected expression before ] token.

WcActCB.c:1536: error: expected = , , , ;, asm or __attribute__ before already.

WcActCB.c:1536: error: already undeclared (first use in this function).

make[2]: *** [WcActB.o] Error 1.

make[2]: Leaving dir '/usr/local/amber9/src/leap/src/Wc'

make [1]: *** [install] Error 2

make[1]: Leaving dir '/usr/local/amber9/src/leap'

make: *** [serial] Error 2
_____________________--

If relevant, I have seen during the process calling "gcc" and "g++" (for
openmpi I have used intel for both fortran, C and C++).
__________________

I don't see any log file in either amber9 or its subdir src. Should I run any
test after such exit?

>
> If you get ifort not found then make sure you have modified your ~/.bashrc
> or ~/.cshrc (depending on your shell) to source
> /opt/intel/fce/9.1.036/bin/ifortvars.sh (or .csh if c shell)

All intel compilers are activated from .bashrc.

Then

cd $AMBEROME/test

make test.serial

All PASSED except leap:

cd leap: ./Run.tleap

Error: ./tleap -> ../../exe/teLeap does not exit

make: *** [test.leap] Error 1
__________________-----

What do you suggest I should do? Can the machine be shutdown and restartd
tomorrow?

Thanks

francesco

>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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