Hi AMBER gurus,
OK the plot thickens....
In my blind ambition to make things work....
I noticed that I have a this file and message:
bzlib.compile.err
testp.c:2:19: fatal error: bzlib.h: No such file or directory
#include "bzlib.h"
^
compilation terminated.
But not deterred I went into the $AMBERHOME/AmberTools/src/leap folder and run make
But it threw and error
make[1]: %AMBERHOME/bin/yacc: command not found
question is why isn't yacc being installed. Is this solely down to the previous error about bzlib.
Thoughts welcome - I'm still here 😊
Best,
mike
Dr Mike Mazanetz, FRSC
Director
+44 (0) 1235 531048
+44 (0) 7780 672509
mikem.novadatasolutions.co.uk
www.novadatasolutions.co.uk
NovaData Solutions Ltd.
PO Box 639
Abingdon-on-Thames
Oxfordshire
OX14 9JD
United Kingdom
-----Original Message-----
From: Mike Mazanetz [mailto:mikem.novadatasolutions.co.uk]
Sent: 06 February 2018 18:00
To: 'AMBER Mailing List' <amber.ambermd.org>
Subject: Re: [AMBER] how to run/install leap
Dear AMBER Forum,
Further to my last email, I thought I'd send some more information:
./Run.tleap
Throws this message:
building force field libraries:
'94 ff..
./Run.tleap: Program error in leap
There is only this file output:
lib94.out
contents are:
/home/ws/NovaData/Software/AMBER/amber16/bin/tleap: Command not found.
I suspect that I've got to build leap somehow?
Here's the output from the command
(./configure -cuda gnu 2>&1) | tee amber-config_cuda.log
Checking for updates...
Checking for available patches online. This may take a few seconds...
Available AmberTools 17 patches:
No patches available
Available Amber 16 patches:
No patches available
AMBER_PREFIX=/home/ws/NovaData/Software/AMBER/amber16
AMBER_SOURCE=/home/ws/NovaData/Software/AMBER/amber16
Compatible Python found! Using
CUDA Version 8.0 detected
Configuring for SM2.0, SM3.0, SM5.0, SM5.2, SM5.3, SM6.0 and SM6.1 BE AWARE: CUDA 8.0 does not support V100, Volta Gefore / GTX Ampere? or other Volta based GPUs.
Obtaining the gnu compiler suite versions, e.g.:
gcc -v
The C version is 4.8.5
The Fortran version is 4.8.5
Testing the gcc compiler:
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c OK
Testing the g++ compiler:
g++ -fPIC -o testp testp.cpp
OK
Testing the gfortran compiler:
gfortran -fPIC -O0 -o testp testp.f OK
Testing mixed C/Fortran compilation:
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o testp.c
gfortran -fPIC -O0 -c -o testp.f.o testp.f
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o testp.f.o -lgfortran -w OK
Testing pointer size:
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size test_pointer_size.c Detected 64 bit operating system.
Testing flex: OK
Checking NetCDF...
Using bundled NetCDF library.
Using existing NetCDF in '/home/ws/NovaData/Software/AMBER/amber16'
Checking for zlib: OK
Checking for libbz2:
Warning: Could not link to libbz2. Ensure libbz2 libraries/headers are installed.
Warning: Failed command:
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -lbz2 -o testp testp.c
Warning: Check bzlib.compile.err for error details.
Warning: Bzip2 compression/decompression not available.
Configuring fftw-3.3 (may be time-consuming)...
fftw-3.3 configure succeeded.
Configuring CPPTRAJ...complete.
Warning: without the Python development libraries and headers you
will not be able to build the Python-sander interface or
pytraj. If you have no need for either, this is not a problem.
The configuration file, config.h, was successfully created.
----------------------------------------------------------------------------
----
Environment resource files are provided to set the proper environment variables to use AMBER and AmberTools. This is required to run any Python programs (like MMPBSA.py, ParmEd, MCPB.py, and pytraj)
If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the /home/ws/NovaData/Software/AMBER/amber16/amber.sh file in your shell.
Consider adding the line
test -f /home/ws/NovaData/Software/AMBER/amber16/amber.sh && source /home/ws/NovaData/Software/AMBER/amber16/amber.sh
to your startup file (e.g., ~/.bashrc)
If you use a C shell (e.g., csh, tcsh), source the /home/ws/NovaData/Software/AMBER/amber16/amber.csh file in your shell.
Consider adding the line
test -f /home/ws/NovaData/Software/AMBER/amber16/amber.csh && source /home/ws/NovaData/Software/AMBER/amber16/amber.csh
to your startup file (e.g., ~/.cshrc)
NOTE: MacOS users might need to add the content to ~/.bash_profile file (You need to do the above before running 'make install')
If you have not already done so, you may need to add /usr/local/cuda/lib and/or /usr/local/cuda/lib64 to LD_LIBRARY_PATH using the command
export LD_LIBRARY_PATH="/usr/local/cuda/lib:${LD_LIBRARY_PATH}" (bash, sh)
setenv LD_LIBRARY_PATH "/usr/local/cuda/lib:${LD_LIBRARY_PATH}" (tcsh,
csh)
----------------------------------------------------------------------------
----
The next step is to source the amber.sh or amber.csh file
(if needed, see above), and then to type 'make install'
Cleaning the src directories. This may take a few moments.
Configure complete.
I see that there is a warning for the libbz2 libraries/headers, but curiously the package for bzip2-libs is up-to-date?
Any thoughts here are also welcome.
-----Original Message-----
From: Mike Mazanetz [mailto:mikem.novadatasolutions.co.uk]
Sent: 06 February 2018 16:40
To: amber.ambermd.org
Subject: [AMBER] how to run/install leap
Dear Forum,
Ok - so I've followed the AMBER 17 manual and completed the AMBER install, everying PASSED.
But I can not find any instructions as to how to then proceed to run LeAP.
I assume that the install built AMBERTOOLS ?
I'd welcome any assistance as to what to do next.
Sorry for being a newbie - I'm on CentOS 7, compiled with ./configure -cuda gnu
Cheers,
Mike
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Received on Tue Feb 06 2018 - 11:30:03 PST
