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From: <[email protected]> on behalf of CUNIASSE Philippe <[email protected]>
Date: Wednesday, 3 May 2023 at 15:09
To: "[email protected]" <[email protected]>
Subject: [phenixbb] Pb installing cryo_fit gromacs

 

Dear all,

I tried to install Cryo_fit on my labtop Macbook pro M1 running OSX 13.0.

The installation of the Cryo_fit itself in Phenix went well.

I then tried to install gromacs (gromacs-4.5.5_cryo_fit) following the instructions found on https://phenix-online.org/documentation/tutorials/cryo_fit_install.html#id1

But during the compilation, I encoutered the following error that stops the process.

 

cc  -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 -I../../include -DGMXLIBDIR=\"/Applications/phenix-1.20.1-4487/modules/cryo_fit/cryo_fit/share/top\"   -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -std=gnu99  -I./include -MT md.o -MD -MP -MF .deps/md.Tpo -c -o md.o md.c

md.c:414:9: error: call to undeclared function 'please_cite'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]

        please_cite(stderr,"Kim2019");

        ^

md.c:421:23: warning: passing 'const char *' to parameter of type 'char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]

    init_em_map(fplog,ftp2fn(efEMM, nfile, fnm), emmap, ir, state_global,cr);

                      ^~~~~~~~~~~~~~~~~~~~~~~~~

../../include/cryoem.h:43:44: note: passing argument to parameter 'emfile' here

extern void init_em_map(FILE *fplog, char *emfile,t_emmap *emmap, t_inputrec *ir, t_state *state, t_commrec *cr);

                                           ^

1 warning and 1 error generated.

 

I did it under a bash shell,

Python version : 2.7.15

 

cc --version

Apple clang version 14.0.3 (clang-1403.0.22.14.1)

Target: arm64-apple-darwin22.1.0

Thread model: posix

InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

 

Any suggestion to solve it ?

Thanks in advance for your help.

Philippe.