[Dock-fans] Installation of DOCK 6.6 on a Mac

Scott Brozell sbrozell at rci.rutgers.edu
Tue Jan 28 11:12:59 PST 2014


Hi,

So the gcc and gfortran versions are the same which indicates
a different problem than in 
http://mailman.docking.org/pipermail/dock-fans/2013-December/002868.html

In the absence of help from actual mac users, i see 3 options:
1.  Double check with a clean rebuild:
cd dock/install; make distclean; configure gnu; make install

Assuming this fails as below, either of these could be tried:

2.  Patch (or hand edit) dock to avoid tnt using the attached no_score_chemgrid.dif:
cd dock/src/dock; patch no_score_chemgrid.dif
cd dock/install; make distclean; configure gnu; make install

3.  Re set up your Mac for scientific computing using a trusted source:
http://jswails.wikidot.com/mac-os-x

scott

On Tue, Jan 28, 2014 at 01:02:57PM +0000, msmith at mcdaniel.edu wrote:
> Hi - Here is the output from both:
> 
> msmithmac:install marilynsmith$ gcc -v
> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
> --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms
> /MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/c++/4.2.1
> Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
> Target: x86_64-apple-darwin13.0.0
> Thread model: posix
> msmithmac:install marilynsmith$ gfortran -v
> Using built-in specs.
> COLLECT_GCC=gfortran
> COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-apple-darwin13.0.0/4.9.0/
> lto-wrapper
> Target: x86_64-apple-darwin13.0.0
> Configured with: ../gcc-4.9-20131215/configure
> --enable-languages=c++,fortran
> Thread model: posix
> gcc version 4.9.0 20131215 (experimental) (GCC)
> 
> On 1/28/14, 3:12 AM, "Scott Brozell" <sbrozell at rci.rutgers.edu> wrote:
> >On Mon, Jan 27, 2014 at 06:30:02PM +0000, msmith at mcdaniel.edu wrote:
> >> This is Chris again, trying to help Marilyn get this thing going. In
> >>order
> >> to be as close to the situation that is in the link that you provided,
> >>we
> >> upgraded from 10.8.5 to 10.9.1 and downloaded the 4.9 version of GCC. We
> >> downloaded the installer for DOCK6 again and tried recompiling and we
> >>get
> >> the exact same result. Really not sure where to go from here, so if you

> >> On 1/24/14, 10:24 PM, "Scott Brozell" <sbrozell at rci.rutgers.edu> wrote:
> >> >On Fri, Jan 24, 2014 at 06:45:15PM +0000, msmith at mcdaniel.edu wrote:
> >> >> I am a tech who is trying to help Marilyn get this installation
> >>figured
> >> >>out. Here is the full output of the command with the warnings and
> >>errors
> >> >>highlighted. Does that give you any more to go on in helping us to
> >> >>figure out where this is getting hung up?
> >> >> 
> >> >> Starting installation of
> >> >> DOCK v6.6
> >> >> at Fri Jan 24 13:37:26 EST 2014.
> >> >> 
> >> >> cd ../src && make install
> >> >> cd dock && make install
> >> >> g++ -c -O2 -o score_chemgrid.o score_chemgrid.cpp
> >> >> In file included from score_chemgrid.cpp:38:
> >> >> In file included from ./tnt/tnt.h:41:
> >> >> ./tnt/tnt_array1d.h:238:15: warning: '&&' within '||'
> >> >>[-Wlogical-op-parentheses]
> >> >> if ((i0 > 0) && (i1 < n_) || (i0 <= i1))
> >> >> ~~~~~~~~~^~~~~~~~~~~~ ~~
> >> >> ./tnt/tnt_array1d.h:238:15: note: place parentheses around the '&&'
> >> >>expression to silence this warning
> >> >...
> >> >> In file included from score_chemgrid.cpp:38:
> >> >> In file included from ./tnt/tnt.h:55:
> >> >> ./tnt/tnt_sparse_matrix_csr.h:97:3: error: no matching constructor
> >>for
> >> >>initialization of 'Array1D<int>'
> >> >> rowptr_(M, r), colind_(nz, c), dim1_(M), dim2_(N) {}
> >> >> ^ ~~~~
> >> >> ./tnt/tnt_array1d.h:63:11: note: candidate constructor not viable: no
> >> >>known conversion from 'const int *' to
> >> >> 'const int' for 2nd argument; dereference the argument with *
> >> >> Array1D(int n, const T &a);
> >> >> ^
> >> >> ./tnt/tnt_array1d.h:64:11: note: candidate constructor not viable:
> >>2nd
> >> >>argument ('const int *') would lose
> >> >> const qualifier
> >> >> Array1D(int n, T *a);
> >> >> ^
> >> >> ./tnt/tnt_array1d.h:61:11: note: candidate constructor not viable:
> >> >>requires 0 arguments, but 2 were provided
> >> >> Array1D();
> >> >> ^
> >> >> ./tnt/tnt_array1d.h:62:11: note: candidate constructor not viable:
> >> >>requires single argument 'n', but 2
> >> >> arguments were provided
> >> >> explicit Array1D(int n);
> >> >> ^
> >> >> ./tnt/tnt_array1d.h:65:14: note: candidate constructor not viable:
> >> >>requires single argument 'A', but 2
> >> >> arguments were provided
> >> >> inline Array1D(const Array1D &A);
> >> >> ^
> >> >...
> >> >> 2 warnings and 2 errors generated.
> >> >> make[2]: *** [score_chemgrid.o] Error 1
> >> >> make[1]: *** [dock6] Error 2
> >> >
> >> >The errors above are the same as those reported in an attachement to
> >> 
> >>>http://mailman.docking.org/pipermail/dock-fans/2013-December/002868.html
> >> >wherein the user reported that the source of the problem was an
> >> >inconsistent
> >> >compiler installation; the fix was to install a newer version at
> >> >http://hpc.sourceforge.net
> >> >
> >> >For my interest, please report the versions you have:
> >> >% gcc -v
> >> >% gfortran -v
-------------- next part --------------
===================================================================
RCS file: /usr/local/cvsroot/dock6/src/dock/Makefile,v
retrieving revision 1.25
diff -c -r1.25 Makefile
*** Makefile	29 Jul 2012 00:35:01 -0000	1.25
--- Makefile	28 Jan 2014 19:01:37 -0000
***************
*** 10,16 ****
        dockmol.o filter.o grid.o hungarian.o library_file.o master_score.o orient.o \
        sasa.o score_amber.o score.o score_descriptor.o score_multigrid.o score_sasa.o score_solvent.o \
        simplex.o sphere.o \
!       score_chemgrid.o utils.o trace.o
  
  all:  $(PROGS)
  
--- 10,16 ----
        dockmol.o filter.o grid.o hungarian.o library_file.o master_score.o orient.o \
        sasa.o score_amber.o score.o score_descriptor.o score_multigrid.o score_sasa.o score_solvent.o \
        simplex.o sphere.o \
!       utils.o trace.o
  
  all:  $(PROGS)
  
===================================================================
RCS file: /usr/local/cvsroot/dock6/src/dock/master_score.cpp,v
retrieving revision 1.25
diff -c -r1.25 master_score.cpp
*** master_score.cpp	28 Jul 2012 23:26:11 -0000	1.25
--- master_score.cpp	28 Jan 2014 19:01:37 -0000
***************
*** 72,80 ****
          c_mg_nrg.use_score = false;
          c_mg_nrg.use_primary_score = false;
          c_mg_nrg.use_secondary_score = false;
!         c_cmg.use_score = false;
!         c_cmg.use_primary_score = false;
!         c_cmg.use_secondary_score = false;
          c_cont_nrg.use_score = false;
          c_cont_nrg.use_primary_score = false;
          c_cont_nrg.use_secondary_score = false;
--- 72,80 ----
          c_mg_nrg.use_score = false;
          c_mg_nrg.use_primary_score = false;
          c_mg_nrg.use_secondary_score = false;
! //        c_cmg.use_score = false;
! //        c_cmg.use_primary_score = false;
! //        c_cmg.use_secondary_score = false;
          c_cont_nrg.use_score = false;
          c_cont_nrg.use_primary_score = false;
          c_cont_nrg.use_secondary_score = false;
***************
*** 159,165 ****
              }
          }
  
! 
          if ((!primary_score_found) || (!secondary_score_found)) {
              c_cmg.input_parameters(parm, primary_score_found,
                                     secondary_score_found);
--- 159,165 ----
              }
          }
  
! /*
          if ((!primary_score_found) || (!secondary_score_found)) {
              c_cmg.input_parameters(parm, primary_score_found,
                                     secondary_score_found);
***************
*** 175,181 ****
                  read_vdw = true;
              }
          }
! 
          if ((!primary_score_found) || (!secondary_score_found)) {
              c_cont_nrg.input_parameters(parm, primary_score_found,
                                          secondary_score_found);
--- 175,181 ----
                  read_vdw = true;
              }
          }
! */
          if ((!primary_score_found) || (!secondary_score_found)) {
              c_cont_nrg.input_parameters(parm, primary_score_found,
                                          secondary_score_found);
***************
*** 348,356 ****
              c_mg_nrg.initialize(typer);
          }
  
!         if (c_cmg.use_score == true) {
!             c_cmg.initialize(typer);
!         }
  
          if (c_cont_nrg.use_score == true) {
              c_cont_nrg.initialize(typer);
--- 348,356 ----
              c_mg_nrg.initialize(typer);
          }
  
! //        if (c_cmg.use_score == true) {
! //            c_cmg.initialize(typer);
! //        }
  
          if (c_cont_nrg.use_score == true) {
              c_cont_nrg.initialize(typer);
===================================================================
RCS file: /usr/local/cvsroot/dock6/src/dock/master_score.h,v
retrieving revision 1.19
diff -c -r1.19 master_score.h
*** master_score.h	28 Jul 2012 23:26:11 -0000	1.19
--- master_score.h	28 Jan 2014 19:01:37 -0000
***************
*** 6,12 ****
  #include "score_multigrid.h"
  #include "score_descriptor.h"
  #include "score_amber.h"
! #include "score_chemgrid.h"
  #include "score_solvent.h"
  #include "score_sasa.h"
  
--- 6,12 ----
  #include "score_multigrid.h"
  #include "score_descriptor.h"
  #include "score_amber.h"
! //#include "score_chemgrid.h"
  #include "score_solvent.h"
  #include "score_sasa.h"
  
***************
*** 16,22 ****
      Base_Score      c_bas; //TEB 2010-03-31
      Energy_Score    c_nrg;
      Multigrid_Energy_Score    c_mg_nrg;
!     Chemgrid_Score  c_cmg;      // kxr & bks scoring 
      Continuous_Energy_Score c_cont_nrg;
      Descriptor_Energy_Score c_desc_nrg;
      Contact_Score   c_cnt;
--- 16,22 ----
      Base_Score      c_bas; //TEB 2010-03-31
      Energy_Score    c_nrg;
      Multigrid_Energy_Score    c_mg_nrg;
! //    Chemgrid_Score  c_cmg;      // kxr & bks scoring 
      Continuous_Energy_Score c_cont_nrg;
      Descriptor_Energy_Score c_desc_nrg;
      Contact_Score   c_cnt;


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