fpocket: Make fails on Fedora 28

Hi,

Make works for a while, then fails on my 64bit Fedora 28 machine with the following output:

… gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/mdparams.c -o obj/mdparams.o gcc obj/mdpmain.o obj/mdpocket.o obj/mdpbase.o obj/mdpout.o obj/psorting.o obj/pscoring.o obj/mdparams.o obj/voronoi.o obj/sort.o obj/rpdb.o obj/descriptors.o obj/neighbor.o obj/atom.o obj/aa.o obj/pertable.o obj/calc.o obj/utils.o obj/writepdb.o obj/memhandler.o obj/pocket.o obj/refine.o obj/fparams.o obj/fpocket.o obj/fpout.o obj/writepocket.o obj/write_visu.o obj/asa.o obj/voronoi_lst.o obj/clusterlib.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o obj/energy.o obj/topology.o -o bin/mdpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++ obj/mdpocket.o: In function mdpocket_detect': /home/christian/Downloads/fpocket/src/mdpocket.c:96: undefined reference to molfile_netcdfplugin_init’ /home/christian/Downloads/fpocket/src/mdpocket.c:97: undefined reference to `molfile_netcdfplugin_register’ collect2: error: ld returned 1 exit status make: *** [makefile:145: bin/mdpocket] Error 1

gcc: 8.1.1-1 netcdf-devel: 4.4.1.1-9

Any ideas what’s wrong? Thanks, Christian

About this issue

Original URL
State: closed
Created 6 years ago
Comments: 36 (12 by maintainers)

Most upvoted comments

Hello! I’ve managed to build the whole package with full NetCDF support. Newer vmd-molfile-plugins are needed (I’ve used 1.9.3 version). You could check my AUR package here. In few words: you should modify makefile like that (patch-friendly):

--- makefile	2019-03-29 00:31:30.876920063 +0300
+++ makefile.new	2019-03-29 00:29:17.804365698 +0300
@@ -34,11 +34,11 @@
 CDEBUG      = -DMNO_MEM_DEBUG
 CWARN       = -Wall -Wextra -Wwrite-strings -Wstrict-prototypes
 
-CFLAGS      = $(CWARN) $(COS) $(CDEBUG) -O2 -g -pg -std=c99 -I$(PLUGINDIR)/include -I$(PLUGINDIR)/$(ARCH)/molfile #$(CGSL)
+CFLAGS      = $(CWARN) $(COS) $(CDEBUG) -O2 -g -pg -std=c99 -I$(PLUGINDIR)/include -I/usr/include/vmd-molfile-plugins/ #$(CGSL)
 QCFLAGS     = -O -g -pg -ansi
 
 LGSL        = -L$(PATH_GSL)lib -lgsl -lgslcblas 
-LFLAGS	    = -lm -L$(PLUGINDIR)/$(ARCH)/molfile $(PLUGINDIR)/$(ARCH)/molfile/libmolfile_plugin.a -lnetcdf -lstdc++
+LFLAGS	    = -lm -L/usr/lib/vmd-molfile-plugins /usr/lib/vmd-molfile-plugins/libmolfile_plugin.a -lnetcdf -lstdc++
 #
 #------------------------------------------------------------
 # BINARIES OBJECTS

dvdesolve on Mar 28, 2019

Hi the make doesn’t work on ubuntu 16.04 LTS (on my 64 bit machine)also. I wish to use mdpocket. I replaced the LINUXAMD64 folder in the plugins directory and rebuild as suggested above but it did’nt worked but got following error during installation of fpocket3 :

obj/mdpocket.o: In function mdpocket_detect': /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:96: undefined reference to molfile_netcdfplugin_init’ /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:97: undefined reference to `molfile_netcdfplugin_register’ collect2: error: ld returned 1 exit status makefile:145: recipe for target ‘bin/mdpocket’ failed make: *** [bin/mdpocket] Error 1

ektapathak08 on Jul 21, 2018