[phenixbb] Pb installing cryo_fit gromacs

[Luca Jovine]

Hi Philippe,
It’s not an optimal workaround, but you can try using CFLAGS="-Wno-error=implicit-function-declaration" …
Best, Luca

-

Luca Jovine, Ph.D.
Professor of Structural Biology, Member of EMBO and the Nobel Assembly
Karolinska Institutet
Department of Biosciences and Nutrition
Medicinaren 25 Neo
Blickagången 16, SE-141 83 Huddinge, Sweden
E-mail: luca.jovine at ki.se
W3: http://jovinelab.org

From: <phenixbb-bounces at phenix-online.org> on behalf of CUNIASSE Philippe <Philippe.CUNIASSE at cea.fr>
Date: Wednesday, 3 May 2023 at 15:09
To: "phenixbb at phenix-online.org" <phenixbb at phenix-online.org>
Subject: [phenixbb] Pb installing cryo_fit gromacs

You don't often get email from philippe.cuniasse at cea.fr. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification>
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.


-----------------------------------------------
Philippe Cuniasse, PhD/HDR.
Institut de Biologie Integrative de la cellule.
UMR 9198 CNRS-CEA-Univ Paris Sud
Bat 144 CE-Saclay
91191 Gif-sur-Yvette Cedex
France
Tel:      (33) 1 69 08 56 35
Fax:      (33) 1 69 08 47 12
Email: philippe.cuniasse at cea.fr<mailto:philippe.cuniasse at cea.fr>
Web: http://biodev.cea.fr/rasmot3d/

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