VMD-L Mailing List

From: Alexander Beerhoff (emserfo_at_gmail.com)
Date: Tue Mar 07 2023 - 19:55:15 CST

I use vmd-1.9.4a57. Building with suggested configuration result in this
error:

In file included from colvarproxy.h:19,
                 from colvarscript.h:20,
                 from colvarproxy_vmd.C:21:
colvarproxy_tcl.h:21:14: error: conflicting declaration 'typedef void
Tcl_Interp'
   21 | typedef void Tcl_Interp;
      | ^~~~~~~~~~
In file included from colvarproxy_vmd.C:10:
/opt/local/include/tcl.h:540:1: note: previous declaration as 'typedef
struct Tcl_Interp Tcl_Interp'
  540 | Tcl_Interp;
      | ^~~~~~~~~~
colvarproxy_vmd.C: In function 'int tcl_colvars(ClientData, Tcl_Interp*,
int, Tcl_Obj* const*)':
colvarproxy_vmd.C:52:10: error: 'tcl_run_colvarscript_command' was not
declared in this scope; did you mean 'run_colvarscript_command'?
   52 | return tcl_run_colvarscript_command(clientData, interp, objc,
objv);
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
      | run_colvarscript_command
make: *** [colvarproxy_vmd.o] Error 1

There could be conflict with tcl8.6.13 in /opt (I use macport/brew to
fullfill deps)?

Best regards

On Tue, Mar 7, 2023 at 7:57 PM John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> What rev of the VMD source are you compiling against?
>
> Also, what hardware are you planning to run on? I ask because I'm not
> aware
> of any existing Macs that have CPUs that support AVX-512 instructions?
> Additionally, in the latest revs of the VMD code, a more appropriate choice
> would be to enable the configure flag "CPUDISPATCH" which does a
> runtime-determined launch of CPU-specific vector-optimized kernels for
> SSE, AVX, AVX2, or AVX-512 (and similarly NEON, or SVE on ARM chips).
>
> The MPI flag and features aren't likely to be useful on MacOS, IMHO.
> Don't use LIBOSPRAY2, it's an experimental branch that doesn't match the
> revs of OSPRay you'd normally encounter.
>
> The normal configure flag set I use for recent VMD builds on MacOS X is:
> MACOSXX86_64 FLTKOPENGL FLTK TK ACTC CPUDISPATCH IMD LIBOSPRAY
> LIBTACHYON COLVARS TCL PTHREADS SILENT LP64
>
> I'm not sure why you're getting the MSMS related errors below, but
> I would guess that this may be due to an unusual (thus not well tested)
> combination of configuration options that aren't normally used together
> on the MacOS build targets.
>
> Try using the standard flag set I suggest above, and once that works, you
> can make some incremental changes and it should be easier to track down any
> remaining issues you may still encounter.
>
> Best,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Mar 07, 2023 at 03:56:42PM +0100, Alexander Beerhoff wrote:
> > Hi,
> > I'm building VMD on MacOs Ventura. I have this error:
> > Compiling DrawMolItemMSMS.C --> DrawMolItemMSMS.o ...
> > clang: warning: argument unused during compilation: '-L/opt/local/lib'
> > [-Wunused-command-line-argument]
> > clang: warning: argument unused during compilation:
> > '-L/usr/local/Cellar/ospray/2.10.0/lib' [-Wunused-command-line-argument]
> > clang: warning: argument unused during compilation:
> > '-L/Users/myusers/vmd-1.9.4a/vmd-plugins/MACOSXX86_64/molfile'
> > [-Wunused-command-line-argument]
> > DrawMolItemMSMS.C:46:5: error: use of undeclared identifier 'msms'
> > msms.clear();
> > ^
> > DrawMolItemMSMS.C:100:19: error: use of undeclared identifier 'msms'
> > msms.compute_from_file(radius, density, count, ids,
> xyzr,
> > flgs));
> > ^
> > DrawMolItemMSMS.C:103:19: error: use of undeclared identifier 'msms'
> > msms.compute_from_socket(radius, density, count, ids,
> > xyzr, flgs));
> > ^
> > DrawMolItemMSMS.C:117:18: error: use of undeclared identifier 'msms'
> > if (msms_ok && msms.faces.num() > 0) {
> > I'm diving into sources files but from my poor C++ knowledge msms is
> > defined in MSMSInterface.C:
> > const char *MSMSInterface::server_name(void) {
> > const char *msms = getenv("MSMSSERVER");
> > if (!msms) {
> > #ifdef _MSC_VER
> > msms = "msms.exe";
> > #else
> > msms = "msms";
> > #endif
> > }
> >
> > return msms;
> > }
> > Don't know if server_name is called before DrawMolItemMSMS.C; where is
> the
> > problem?
> >
> > I'm using this configure.options:
> > MACOSXX86_64 OPENGL OPENGLPBUFFER FLTK TK ACTC AVX512 MPI XINERAMA
> > LIBOSPRAY2 LIBTACHYON LIBPNG LINENOISE ZLIB VRPN NETCDF TCL PYTHON
> PTHREADS
> > NUMPY
> > Thank you
> > --
> > Umi sukoschi
> > Niwa ni izumi no
> > Ko no ma ka na
>
>
> --
> Research Affiliate, NIH Center for Macromolecular Modeling and
> Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/
> http://www.ks.uiuc.edu/Research/vmd/
> 

-- 
Umi sukoschi
Niwa ni izumi no
Ko no ma ka na