[Dock-fans] Error message on installation

Scott Brozell sbrozell at rci.rutgers.edu
Tue Jun 14 22:56:55 PDT 2016


Hi,

Please provide your system details for platforms for which you cannot
compile dock6.mpi so that we can consider those for our development testing.

FWIW, i routinely build dock6.mpi with gnu compiler versions 4 and 5
on linux platforms such as redhat.

thanks,
scott

E.g.:
gcc version 4.4.7 20120313 (Red Hat 4.4.7-16) (GCC) 
Red Hat Enterprise Linux Server release 6.7 (Santiago)
Linux 2.6.32-573.3.1.el6.x86_64 #1 SMP Mon Aug 10 09:44:54 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux

On Tue, Jun 14, 2016 at 09:22:11PM +0000, Julio Dominguez wrote:
> FYI, to compile dock in MPI I have only been successful using Intel compilers. If anybody has those and want me to share my config file just let me know.
> Best regards
> 
> Date: Fri, 25 Sep 2015 17:13:04 -0400
> From: dwight.mcgee at gmail.com
> To: sbrozell at rci.rutgers.edu
> CC: res48 at leicester.ac.uk; dock-fans at docking.org
> Subject: Re: [Dock-fans] Error message on installation
> 
> Hi,
> 
> I also have the OSX Yosemite and I have been able to successfully compile DOCK6.7 on my MAC using GCC 4.8, which I installed through macports. 
> 
> If you wanted to used the compilers built by macports you can follow the link (jason swails wiki) that Scott posted in his previous email.
> 
> 
> Best,
> Dwight
> 
> On Fri, Sep 25, 2015 at 4:45 PM, Scott Brozell <sbrozell at rci.rutgers.edu> wrote:
> Hi,
> 
> 
> 
> Your compiler versions are inconsistent:
> 
> > Apple LLVM version 7.0.0 (clang-700.0.72)
> 
> > gcc version 5.1.0 (GCC)
> 
> 
> 
> I suggest that you follow the general mac help here:
> 
> http://dock.compbio.ucsf.edu/DOCK_6/faq.htm#macosx
> 
> Namely, start over and get a solid Mac OS X set up for computational chemistry:
> 
> http://jswails.wikidot.com/mac-os-x
> 
> http://macinchem.org/reviews/cheminfo/cheminfoMac.php
> 
> 
> 
> Others on the list that actually build comp chem software on macs may be
> 
> able to offer you more particular help.
> 
> 
> 
> scott
> 
> 
> 
> On Fri, Sep 25, 2015 at 12:35:34PM +0000, Shaikh, Ra'eesah wrote:
> 
> > I have both gfortran and gcc compilers.
> 
> > ___
> 
> > I installed using
> 
> > % ./configure gnu
> 
> > % make all
> 
> > ___
> 
> >
> 
> > The following is the error message.
> 
> >
> 
> > ___
> 
> > 2 warnings and 2 errors generated.
> 
> > make[2]: *** [score_chemgrid.o] Error 1
> 
> > make[1]: *** [dock6] Error 2
> 
> > make: *** [install] Error 2
> 
> > ____
> 
> >
> 
> >
> 
> > host-194-40:~ raeesahshaikh$ gcc -v
> 
> > Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
> 
> > Apple LLVM version 7.0.0 (clang-700.0.72)
> 
> > Target: x86_64-apple-darwin14.5.0
> 
> > Thread model: posix
> 
> >
> 
> > host-194-40:~ raeesahshaikh$ gfortran -v
> 
> > Using built-in specs.
> 
> > COLLECT_GCC=gfortran
> 
> > COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-apple-darwin14.4.0/5.1.0/lto-wrapper
> 
> > Target: x86_64-apple-darwin14.4.0
> 
> > Configured with: ../gcc-5.1.0/configure --enable-languages=c++,fortran
> 
> > Thread model: posix
> 
> > gcc version 5.1.0 (GCC)
> 
> >
> 
> > On 24 Sep 2015, at 22:02, Scott Brozell <sbrozell at rci.rutgers.edu<mailto:sbrozell at rci.rutgers.edu>> wrote: >
> 
> >
> 
> > In the past such errors have been due to an awry compiler installation; see
> 
> > http://mailman.docking.org/pipermail/dock-fans/2014-January/002884.html
> 
> >
> 
> > Please report the compilers and versions you have, eg, if gnu then:
> 
> > % gcc -v
> 
> > % gfortran -v
> 
> >
> 
> > See also for general mac help:
> 
> > http://dock.compbio.ucsf.edu/DOCK_6/faq.htm#macosx
> 
> >
> 
> > thanks,
> 
> > scott
> 
> >
> 
> >
> 
> > On Thu, Sep 24, 2015 at 12:09:11PM -0700, John Irwin wrote:
> 
> > forwarded to list
> 
> >
> 
> > ---------- Forwarded message ----------
> 
> > From: Shaikh, Ra'eesah <res48 at leicester.ac.uk>
> 
> >
> 
> > I am having some issues with installing Dock 6.7 on my OS X Yosemite system.
> 
> >
> 
> > The following error message(s) keep appearing:
> 
> >
> 
> > ./tnt/tnt_sparse_matrix_csr.h:97:3: error: no matching constructor for
> 
> >      initialization of 'Array1D<int>???
> 
> >
> 
> > ./tnt/tnt_sparse_matrix_csr.h:97:18: error: no matching constructor for
> 
> >      initialization of 'Array1D<int>???


More information about the Dock-fans mailing list