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Electrostatics / apbs-pdb2pqr

APBS - software for biomolecular electrostatics and solvation
http://www.poissonboltzmann.org/
128 stars 62 forks source link

github apbs compilation issue #526

Closed Vcald closed 4 years ago

Vcald commented 4 years ago

When trying to compile on fedora 30 x64 I get the follwoing error... Any hint?

/usr/bin/cmake -S/mnt/usr/local/apbs-pdb2pqr/apbs -B/mnt/usr/local/apbs-pdb2pqr/apbs --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /mnt/usr/local/apbs-pdb2pqr/apbs/CMakeFiles /mnt/usr/local/apbs-pdb2pqr/apbs/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make -f externals/fetk/maloc/src/CMakeFiles/maloc.dir/build.make externals/fetk/maloc/src/CMakeFiles/maloc.dir/depend cd /mnt/usr/local/apbs-pdb2pqr/apbs && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /mnt/usr/local/apbs-pdb2pqr/apbs /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src /mnt/usr/local/apbs-pdb2pqr/apbs /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/CMakeFiles/maloc.dir/DependInfo.cmake --color= make -f externals/fetk/maloc/src/CMakeFiles/maloc.dir/build.make externals/fetk/maloc/src/CMakeFiles/maloc.dir/build make[2]: Nothing to be done for 'externals/fetk/maloc/src/CMakeFiles/maloc.dir/build'. [ 19%] Built target maloc make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/depend cd /mnt/usr/local/apbs-pdb2pqr/apbs && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /mnt/usr/local/apbs-pdb2pqr/apbs /mnt/usr/local/apbs-pdb2pqr/apbs/src /mnt/usr/local/apbs-pdb2pqr/apbs /mnt/usr/local/apbs-pdb2pqr/apbs/src /mnt/usr/local/apbs-pdb2pqr/apbs/src/CMakeFiles/apbs_routines.dir/DependInfo.cmake --color= make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/build make[2]: Nothing to be done for 'src/CMakeFiles/apbs_routines.dir/build'. [ 21%] Built target apbs_routines make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/depend cd /mnt/usr/local/apbs-pdb2pqr/apbs && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /mnt/usr/local/apbs-pdb2pqr/apbs /mnt/usr/local/apbs-pdb2pqr/apbs/src/pmgc /mnt/usr/local/apbs-pdb2pqr/apbs /mnt/usr/local/apbs-pdb2pqr/apbs/src/pmgc /mnt/usr/local/apbs-pdb2pqr/apbs/src/pmgc/CMakeFiles/apbs_pmgc.dir/DependInfo.cmake --color= make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/build make[2]: Nothing to be done for 'src/pmgc/CMakeFiles/apbs_pmgc.dir/build'. [ 40%] Built target apbs_pmgc make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/depend cd /mnt/usr/local/apbs-pdb2pqr/apbs && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /mnt/usr/local/apbs-pdb2pqr/apbs /mnt/usr/local/apbs-pdb2pqr/apbs/src/generic /mnt/usr/local/apbs-pdb2pqr/apbs /mnt/usr/local/apbs-pdb2pqr/apbs/src/generic /mnt/usr/local/apbs-pdb2pqr/apbs/src/generic/CMakeFiles/apbs_generic.dir/DependInfo.cmake --color= make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/build make[2]: Nothing to be done for 'src/generic/CMakeFiles/apbs_generic.dir/build'. [ 59%] Built target apbs_generic make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/depend cd /mnt/usr/local/apbs-pdb2pqr/apbs && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /mnt/usr/local/apbs-pdb2pqr/apbs /mnt/usr/local/apbs-pdb2pqr/apbs/src/mg /mnt/usr/local/apbs-pdb2pqr/apbs /mnt/usr/local/apbs-pdb2pqr/apbs/src/mg /mnt/usr/local/apbs-pdb2pqr/apbs/src/mg/CMakeFiles/apbs_mg.dir/DependInfo.cmake --color= make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/build make[2]: Nothing to be done for 'src/mg/CMakeFiles/apbs_mg.dir/build'. [ 65%] Built target apbs_mg make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/depend cd /mnt/usr/local/apbs-pdb2pqr/apbs && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /mnt/usr/local/apbs-pdb2pqr/apbs /mnt/usr/local/apbs-pdb2pqr/apbs/src /mnt/usr/local/apbs-pdb2pqr/apbs /mnt/usr/local/apbs-pdb2pqr/apbs/src /mnt/usr/local/apbs-pdb2pqr/apbs/src/CMakeFiles/apbs.dir/DependInfo.cmake --color= make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/build [ 66%] Linking C executable ../bin/apbs cd /mnt/usr/local/apbs-pdb2pqr/apbs/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs.dir/link.txt --verbose=1 /usr/lib64/ccache/cc -O2 -g -DNDEBUG -rdynamic CMakeFiles/apbs.dir/main.c.o CMakeFiles/apbs.dir/routines.c.o -o ../bin/apbs -L/mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/lib -Wl,-rpath,/mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/lib: -lm -lstdc++ ../externals/fetk/maloc/lib/libmaloc.a ../lib/libapbs_generic.a ../lib/libapbs_pmgc.a ../lib/libapbs_mg.a ../lib/libapbs_routines.a -lm -lstdc++ ../externals/fetk/maloc/lib/libmaloc.a ../lib/libapbs_generic.a ../lib/libapbs_pmgc.a -lm -lstdc++ ../externals/fetk/maloc/lib/libmaloc.a /usr/bin/ld: ../externals/fetk/maloc/lib/libmaloc.a(vio.c.o): in function Vio_ctor2': /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:770: undefined reference toxdrmem_create' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:768: undefined reference to xdrmem_create' /usr/bin/ld: ../externals/fetk/maloc/lib/libmaloc.a(vio.c.o): in functionVio_scanf': /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1500: undefined reference to xdr_double' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1452: undefined reference toxdr_string' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1462: undefined reference to xdr_char' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1471: undefined reference toxdr_int' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1489: undefined reference to xdr_float' /usr/bin/ld: ../externals/fetk/maloc/lib/libmaloc.a(vio.c.o): in functionVio_printf': /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1610: undefined reference to xdr_double' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1579: undefined reference toxdr_string' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1603: undefined reference to xdr_float' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1586: undefined reference toxdr_char' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1591: undefined reference to `xdr_int' collect2: error: ld returned 1 exit status make[2]: [src/CMakeFiles/apbs.dir/build.make:111: bin/apbs] Error 1 make[1]: [CMakeFiles/Makefile2:301: src/CMakeFiles/apbs.dir/all] Error 2 make: *** [Makefile:133: all] Error 2

kozlac commented 4 years ago

Hello @Vcald! The build is failing because it's trying build against the RPC library and it doesn't seem to be on your LD path. Could you paste the output of the CMake configuration step? The CMake script checks if the library is present or not and shouldn't have included it if it wasn't present.

Could you please start on a fresh build folder. That is, make a new build folder and run the CMake and make commands there. Thanks!!

Vcald commented 4 years ago

There you go:

git submodule init

Submodule 'apbs/externals/bem' (https://github.com/lwwilson1/TABIPB.git) registered for path 'apbs/externals/bem' Submodule 'apbs/externals/fetk' (https://github.com/Electrostatics/FETK.git) registered for path 'apbs/externals/fetk' Submodule 'apbs/externals/geoflow_c' (https://github.com/Electrostatics/geoflow_c) registered for path 'apbs/externals/geoflow_c' Submodule 'apbs/externals/mesh_routines' (https://github.com/lwwilson1/mesh_routines.git) registered for path 'apbs/externals/mesh_routines' Submodule 'apbs/externals/pb_s_am' (https://github.com/davas301/pb_solvers) registered for path 'apbs/externals/pb_s_am' [vito@PC-STUDIO apbs-pdb2pqr]# git submodule update Cloning into '/mnt/usr/local/apbs-pdb2pqr/apbs/externals/bem'... Cloning into '/mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk'... Cloning into '/mnt/usr/local/apbs-pdb2pqr/apbs/externals/geoflow_c'... Cloning into '/mnt/usr/local/apbs-pdb2pqr/apbs/externals/mesh_routines'... Cloning into '/mnt/usr/local/apbs-pdb2pqr/apbs/externals/pb_s_am'... Submodule path 'apbs/externals/bem': checked out '7e3a407165586e0c17dc7326bff73d733ec70bdc' Submodule path 'apbs/externals/fetk': checked out '0c6fdeabe8929acea7481cb1480b5706b343b7e0' Submodule path 'apbs/externals/geoflow_c': checked out 'e8ce510a670e0b7f3501e72be6141fc20328f947' Submodule path 'apbs/externals/mesh_routines': checked out 'ddb75cb13318714de1d72d3658da372c9b5488d0' Submodule path 'apbs/externals/pb_s_am': checked out '48584653b908a84593016892a18c0a7a46642a76' [vito@PC-STUDIO apbs-pdb2pqr]# cmake apbs CMake Deprecation Warning at CMakeLists.txt:33 (cmake_policy): The OLD behavior for policy CMP0054 will be removed from a future version of CMake.

The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD.

-- The C compiler identification is GNU 9.1.1 -- The CXX compiler identification is GNU 9.1.1 -- Check for working C compiler: /usr/lib64/ccache/cc -- Check for working C compiler: /usr/lib64/ccache/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/lib64/ccache/c++ -- Check for working CXX compiler: /usr/lib64/ccache/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Setting project paths -- Setting lookup paths for headers and libraries -- Computing machine epsilon values -- Floating point epsilon is 2.220446e-16 -- Double precision epsilon is 2.220446e-16 -- Looking for time -- Looking for time - found -- Looking for rand -- Looking for rand - found -- Looking for srand -- Looking for srand - found -- Setting project paths -- Setting lookup paths for headers and libraries -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of mode_t -- Check size of mode_t - done -- Check size of pid_t -- Check size of pid_t - done -- Check size of size_t -- Check size of size_t - done -- Looking for 4 include files stdlib.h, ..., float.h -- Looking for 4 include files stdlib.h, ..., float.h - found -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file sys/stat.h -- Looking for include file sys/stat.h - found -- Looking for include file sys/socket.h -- Looking for include file sys/socket.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file sys/un.h -- Looking for include file sys/un.h - found -- Looking for include file sys/wait.h -- Looking for include file sys/wait.h - found -- Looking for include file fcntl.h -- Looking for include file fcntl.h - found -- Looking for include file netinet/in.h -- Looking for include file netinet/in.h - found -- Looking for include file arpa/inet.h -- Looking for include file arpa/inet.h - found -- Looking for include file netdb.h -- Looking for include file netdb.h - found -- Looking for include file rpc/rpc.h -- Looking for include file rpc/rpc.h - found -- Looking for getcwd -- Looking for getcwd - found -- Looking for O_NONBLOCK -- Looking for O_NONBLOCK - found -- With sources: base/maloc_base.c;psh/psh.c;psh/vcom.c;psh/vmp.c;psh/vmpi.c;vsh/vlex.c;vsh/vpars.c;vsh/vpup.c;vsh/vsh.c;vsh/vyacc.c;vsys/vio.c;vsys/viofb.c;vsys/vmem.c;vsys/vnm.c;vsys/vnmfb.c;vsys/vpred.c;vsys/vset.c;vsys/ziofb.c -- With external headers: base/maloc/maloc.h;base/maloc/maloc_base.h;psh/maloc/psh.h;psh/maloc/vcom.h;psh/maloc/vmp.h;psh/maloc/vmpi.h;vsh/maloc/vsh.h;vsys/maloc/vio.h;vsys/maloc/vmem.h;vsys/maloc/vnm.h;vsys/maloc/vset.h;vsys/maloc/vsys.h;vsys/maloc/vpred.h -- With internal headers: base/maloc_base_p.h;psh/psh_p.h;psh/vcom_p.h;psh/vmpi_p.h;psh/vmp_p.h;vsh/vpup.h;vsh/vsh_p.h;vsh/vyacc.h;vsys/vio_p.h;vsys/vmem_p.h;vsys/vnm_p.h;vsys/vpred_p.h;vsys/vset_p.h -- Inline functions enabled -- Verbose debugging mode enabled -- Adding apbs_generic -- With source files nosh.c;mgparm.c;femparm.c;pbamparm.c;pbsamparm.c;pbeparm.c;bemparm.c;geoflowparm.c;apolparm.c;vacc.c;valist.c;vatom.c;vpbe.c;vcap.c;vclist.c;vstring.c;vparam.c;vgreen.c -- With external header files nosh.h;mgparm.h;femparm.h;pbamparm.h;pbsamparm.h;pbeparm.h;bemparm.h;geoflowparm.h;apolparm.h;vacc.h;valist.h;vatom.h;vpbe.h;vcap.h;vclist.h;vstring.h;vparam.h;vgreen.h;vmatrix.h;vhal.h;vunit.h -- With internal header files -- With library dependencies m;stdc++;maloc -- Added apbs_generic -- Adding apbs_pmgc -- With source files buildAd.c;buildBd.c;buildGd.c;buildPd.c;cgd.c;gsd.c;matvecd.c;mgcsd.c;mgdrvd.c;mgsubd.c;mikpckd.c;mlinpckd.c;mypdec.c;newtond.c;newdrvd.c;powerd.c;smoothd.c;mgfasd.c -- With external header files buildAd.h;buildBd.h;buildGd.h;buildPd.h;cgd.h;gsd.h;matvecd.h;mgcsd.h;mgdrvd.h;mgsubd.h;mikpckd.h;mlinpckd.h;mypdec.h;newtond.h;newdrvd.h;powerd.h;smoothd.h;mgfasd.h -- With internal header files -- With library dependencies m;stdc++;maloc -- Added apbs_pmgc -- Adding apbs_mg -- With source files vgrid.c;vmgrid.c;vopot.c;vpmg.c;vpmgp.c -- With external header files vgrid.h;vmgrid.h;vopot.h;vpmg.h;vpmgp.h -- With internal header files -- With library dependencies m;stdc++;maloc;apbs_generic;apbs_pmgc -- Added apbs_mg -- Adding apbs_routines -- With source files routines.c -- With external header files -- With internal header files -- With library dependencies m;stdc++;maloc -- Added apbs_routines -- --
-- APBS Libraries: m;stdc++;maloc -- Internal Libraries: apbs_generic;apbs_pmgc;apbs_mg;apbs_routines --
-- -- Supplemental tools enabled -- Building mesh -- libraries: apbs_generic;apbs_mg;apbs_pmgc -- Building manip -- libraries: apbs_generic;apbs_mg;apbs_pmgc -- Configuring done -- Generating done -- Build files have been written to: /mnt/usr/local/apbs-pdb2pqr

make

Scanning dependencies of target maloc [ 1%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/base/maloc_base.c.o [ 2%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/psh/psh.c.o [ 3%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/psh/vcom.c.o [ 4%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/psh/vmp.c.o [ 5%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/psh/vmpi.c.o [ 6%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsh/vlex.c.o [ 7%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsh/vpars.c.o [ 8%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsh/vpup.c.o [ 9%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsh/vsh.c.o [ 10%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsh/vyacc.c.o [ 11%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/vio.c.o /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c: In function ‘Vio_ctor2’: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:701:17: warning: ‘memcpy’ reading 8 bytes from a region of size 4 [-Wstringop-overflow=] 701 | memcpy(&((struct sockaddr_in *)(thee->name))->sin_addr, | ^~~~~~~~~~~~~~~ 702 | &n, sizeof(long)); | ~~~~~ [ 12%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/viofb.c.o [ 13%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/vmem.c.o [ 14%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/vnm.c.o [ 15%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/vnmfb.c.o [ 16%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/vpred.c.o [ 17%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/vset.c.o [ 18%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/ziofb.c.o [ 19%] Linking C static library ../../../../apbs/externals/fetk/maloc/lib/libmaloc.a [ 19%] Built target maloc Scanning dependencies of target apbs_routines [ 20%] Building C object src/CMakeFiles/apbs_routines.dir/routines.c.o [ 21%] Linking C static library ../lib/libapbs_routines.a [ 21%] Built target apbs_routines Scanning dependencies of target apbs_pmgc [ 22%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o [ 23%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o [ 24%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o [ 25%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o [ 26%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o [ 27%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o [ 28%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o [ 29%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o [ 30%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o [ 31%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o [ 32%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o [ 33%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o [ 34%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o [ 35%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o [ 36%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o [ 37%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o [ 38%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o [ 39%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o [ 40%] Linking C static library ../../lib/libapbs_pmgc.a [ 40%] Built target apbs_pmgc Scanning dependencies of target apbs_generic [ 41%] Building C object src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o [ 42%] Building C object src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o [ 43%] Building C object src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o [ 44%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o [ 45%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o [ 46%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o [ 47%] Building C object src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o [ 48%] Building C object src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o [ 49%] Building C object src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o [ 50%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o [ 51%] Building C object src/generic/CMakeFiles/apbs_generic.dir/valist.c.o [ 52%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o [ 53%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o [ 54%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o [ 55%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o [ 56%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o [ 57%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o [ 58%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o [ 59%] Linking C static library ../../lib/libapbs_generic.a [ 59%] Built target apbs_generic Scanning dependencies of target apbs_mg [ 60%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o [ 61%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o [ 62%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o [ 63%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o [ 64%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o [ 65%] Linking C static library ../../lib/libapbs_mg.a [ 65%] Built target apbs_mg Scanning dependencies of target apbs [ 66%] Building C object src/CMakeFiles/apbs.dir/main.c.o [ 67%] Building C object src/CMakeFiles/apbs.dir/routines.c.o [ 68%] Linking C executable ../bin/apbs /usr/bin/ld: ../apbs/externals/fetk/maloc/lib/libmaloc.a(vio.c.o): in function Vio_ctor2': /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:769: undefined reference toxdrmem_create' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:767: undefined reference to xdrmem_create' /usr/bin/ld: ../apbs/externals/fetk/maloc/lib/libmaloc.a(vio.c.o): in functionVio_scanf': /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1499: undefined reference to xdr_double' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1451: undefined reference toxdr_string' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1461: undefined reference to xdr_char' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1470: undefined reference toxdr_int' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1488: undefined reference to xdr_float' /usr/bin/ld: ../apbs/externals/fetk/maloc/lib/libmaloc.a(vio.c.o): in functionVio_printf': /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1609: undefined reference to xdr_double' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1578: undefined reference toxdr_string' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1602: undefined reference to xdr_float' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1585: undefined reference toxdr_char' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1590: undefined reference to `xdr_int' collect2: error: ld returned 1 exit status make[2]: [src/CMakeFiles/apbs.dir/build.make:108: bin/apbs] Error 1 make[1]: [CMakeFiles/Makefile2:298: src/CMakeFiles/apbs.dir/all] Error 2 make: *** [Makefile:130: all] Error 2

Vcald commented 4 years ago

There you go:

git submodule init

Submodule 'apbs/externals/bem' (https://github.com/lwwilson1/TABIPB.git) registered for path 'apbs/externals/bem' Submodule 'apbs/externals/fetk' (https://github.com/Electrostatics/FETK.git) registered for path 'apbs/externals/fetk' Submodule 'apbs/externals/geoflow_c' (https://github.com/Electrostatics/geoflow_c) registered for path 'apbs/externals/geoflow_c' Submodule 'apbs/externals/mesh_routines' (https://github.com/lwwilson1/mesh_routines.git) registered for path 'apbs/externals/mesh_routines' Submodule 'apbs/externals/pb_s_am' (https://github.com/davas301/pb_solvers) registered for path 'apbs/externals/pb_s_am' [vito@PC-STUDIO apbs-pdb2pqr]# git submodule update Cloning into '/mnt/usr/local/apbs-pdb2pqr/apbs/externals/bem'... Cloning into '/mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk'... Cloning into '/mnt/usr/local/apbs-pdb2pqr/apbs/externals/geoflow_c'... Cloning into '/mnt/usr/local/apbs-pdb2pqr/apbs/externals/mesh_routines'... Cloning into '/mnt/usr/local/apbs-pdb2pqr/apbs/externals/pb_s_am'... Submodule path 'apbs/externals/bem': checked out '7e3a407165586e0c17dc7326bff73d733ec70bdc' Submodule path 'apbs/externals/fetk': checked out '0c6fdeabe8929acea7481cb1480b5706b343b7e0' Submodule path 'apbs/externals/geoflow_c': checked out 'e8ce510a670e0b7f3501e72be6141fc20328f947' Submodule path 'apbs/externals/mesh_routines': checked out 'ddb75cb13318714de1d72d3658da372c9b5488d0' Submodule path 'apbs/externals/pb_s_am': checked out '48584653b908a84593016892a18c0a7a46642a76' [vito@PC-STUDIO apbs-pdb2pqr]# cmake apbs CMake Deprecation Warning at CMakeLists.txt:33 (cmake_policy): The OLD behavior for policy CMP0054 will be removed from a future version of CMake.

The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD.

-- The C compiler identification is GNU 9.1.1 -- The CXX compiler identification is GNU 9.1.1 -- Check for working C compiler: /usr/lib64/ccache/cc -- Check for working C compiler: /usr/lib64/ccache/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/lib64/ccache/c++ -- Check for working CXX compiler: /usr/lib64/ccache/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Setting project paths -- Setting lookup paths for headers and libraries -- Computing machine epsilon values -- Floating point epsilon is 2.220446e-16 -- Double precision epsilon is 2.220446e-16 -- Looking for time -- Looking for time - found -- Looking for rand -- Looking for rand - found -- Looking for srand -- Looking for srand - found -- Setting project paths -- Setting lookup paths for headers and libraries -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of mode_t -- Check size of mode_t - done -- Check size of pid_t -- Check size of pid_t - done -- Check size of size_t -- Check size of size_t - done -- Looking for 4 include files stdlib.h, ..., float.h -- Looking for 4 include files stdlib.h, ..., float.h - found -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file sys/stat.h -- Looking for include file sys/stat.h - found -- Looking for include file sys/socket.h -- Looking for include file sys/socket.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file sys/un.h -- Looking for include file sys/un.h - found -- Looking for include file sys/wait.h -- Looking for include file sys/wait.h - found -- Looking for include file fcntl.h -- Looking for include file fcntl.h - found -- Looking for include file netinet/in.h -- Looking for include file netinet/in.h - found -- Looking for include file arpa/inet.h -- Looking for include file arpa/inet.h - found -- Looking for include file netdb.h -- Looking for include file netdb.h - found -- Looking for include file rpc/rpc.h -- Looking for include file rpc/rpc.h - found -- Looking for getcwd -- Looking for getcwd - found -- Looking for O_NONBLOCK -- Looking for O_NONBLOCK - found -- With sources: base/maloc_base.c;psh/psh.c;psh/vcom.c;psh/vmp.c;psh/vmpi.c;vsh/vlex.c;vsh/vpars.c;vsh/vpup.c;vsh/vsh.c;vsh/vyacc.c;vsys/vio.c;vsys/viofb.c;vsys/vmem.c;vsys/vnm.c;vsys/vnmfb.c;vsys/vpred.c;vsys/vset.c;vsys/ziofb.c -- With external headers: base/maloc/maloc.h;base/maloc/maloc_base.h;psh/maloc/psh.h;psh/maloc/vcom.h;psh/maloc/vmp.h;psh/maloc/vmpi.h;vsh/maloc/vsh.h;vsys/maloc/vio.h;vsys/maloc/vmem.h;vsys/maloc/vnm.h;vsys/maloc/vset.h;vsys/maloc/vsys.h;vsys/maloc/vpred.h -- With internal headers: base/maloc_base_p.h;psh/psh_p.h;psh/vcom_p.h;psh/vmpi_p.h;psh/vmp_p.h;vsh/vpup.h;vsh/vsh_p.h;vsh/vyacc.h;vsys/vio_p.h;vsys/vmem_p.h;vsys/vnm_p.h;vsys/vpred_p.h;vsys/vset_p.h -- Inline functions enabled -- Verbose debugging mode enabled -- Adding apbs_generic -- With source files nosh.c;mgparm.c;femparm.c;pbamparm.c;pbsamparm.c;pbeparm.c;bemparm.c;geoflowparm.c;apolparm.c;vacc.c;valist.c;vatom.c;vpbe.c;vcap.c;vclist.c;vstring.c;vparam.c;vgreen.c -- With external header files nosh.h;mgparm.h;femparm.h;pbamparm.h;pbsamparm.h;pbeparm.h;bemparm.h;geoflowparm.h;apolparm.h;vacc.h;valist.h;vatom.h;vpbe.h;vcap.h;vclist.h;vstring.h;vparam.h;vgreen.h;vmatrix.h;vhal.h;vunit.h -- With internal header files -- With library dependencies m;stdc++;maloc -- Added apbs_generic -- Adding apbs_pmgc -- With source files buildAd.c;buildBd.c;buildGd.c;buildPd.c;cgd.c;gsd.c;matvecd.c;mgcsd.c;mgdrvd.c;mgsubd.c;mikpckd.c;mlinpckd.c;mypdec.c;newtond.c;newdrvd.c;powerd.c;smoothd.c;mgfasd.c -- With external header files buildAd.h;buildBd.h;buildGd.h;buildPd.h;cgd.h;gsd.h;matvecd.h;mgcsd.h;mgdrvd.h;mgsubd.h;mikpckd.h;mlinpckd.h;mypdec.h;newtond.h;newdrvd.h;powerd.h;smoothd.h;mgfasd.h -- With internal header files -- With library dependencies m;stdc++;maloc -- Added apbs_pmgc -- Adding apbs_mg -- With source files vgrid.c;vmgrid.c;vopot.c;vpmg.c;vpmgp.c -- With external header files vgrid.h;vmgrid.h;vopot.h;vpmg.h;vpmgp.h -- With internal header files -- With library dependencies m;stdc++;maloc;apbs_generic;apbs_pmgc -- Added apbs_mg -- Adding apbs_routines -- With source files routines.c -- With external header files -- With internal header files -- With library dependencies m;stdc++;maloc -- Added apbs_routines --

-- APBS Libraries: m;stdc++;maloc -- Internal Libraries: apbs_generic;apbs_pmgc;apbs_mg;apbs_routines

-- -- Supplemental tools enabled -- Building mesh -- libraries: apbs_generic;apbs_mg;apbs_pmgc -- Building manip -- libraries: apbs_generic;apbs_mg;apbs_pmgc -- Configuring done -- Generating done -- Build files have been written to: /mnt/usr/local/apbs-pdb2pqr

make

Scanning dependencies of target maloc [ 1%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/base/maloc_base.c.o [ 2%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/psh/psh.c.o [ 3%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/psh/vcom.c.o [ 4%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/psh/vmp.c.o [ 5%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/psh/vmpi.c.o [ 6%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsh/vlex.c.o [ 7%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsh/vpars.c.o [ 8%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsh/vpup.c.o [ 9%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsh/vsh.c.o [ 10%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsh/vyacc.c.o [ 11%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/vio.c.o /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c: In function ‘Vio_ctor2’: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:701:17: warning: ‘memcpy’ reading 8 bytes from a region of size 4 [-Wstringop-overflow=] 701 memcpy(&((struct sockaddr_in *)(thee->name))->sin_addr,

^~~~~~~~~~~~~~~ 702 | &n, sizeof(long)); | ~~~~~ [ 12%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/viofb.c.o [ 13%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/vmem.c.o [ 14%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/vnm.c.o [ 15%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/vnmfb.c.o [ 16%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/vpred.c.o [ 17%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/vset.c.o [ 18%] Building C object externals/fetk/maloc/src/CMakeFiles/maloc.dir/vsys/ziofb.c.o [ 19%] Linking C static library ../../../../apbs/externals/fetk/maloc/lib/libmaloc.a [ 19%] Built target maloc Scanning dependencies of target apbs_routines [ 20%] Building C object src/CMakeFiles/apbs_routines.dir/routines.c.o [ 21%] Linking C static library ../lib/libapbs_routines.a [ 21%] Built target apbs_routines Scanning dependencies of target apbs_pmgc [ 22%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o [ 23%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o [ 24%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o [ 25%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o [ 26%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o [ 27%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o [ 28%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o [ 29%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o [ 30%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o [ 31%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o [ 32%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o [ 33%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o [ 34%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o [ 35%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o [ 36%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o [ 37%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o [ 38%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o [ 39%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o [ 40%] Linking C static library ../../lib/libapbs_pmgc.a [ 40%] Built target apbs_pmgc Scanning dependencies of target apbs_generic [ 41%] Building C object src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o [ 42%] Building C object src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o [ 43%] Building C object src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o [ 44%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o [ 45%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o [ 46%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o [ 47%] Building C object src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o [ 48%] Building C object src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o [ 49%] Building C object src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o [ 50%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o [ 51%] Building C object src/generic/CMakeFiles/apbs_generic.dir/valist.c.o [ 52%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o [ 53%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o [ 54%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o [ 55%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o [ 56%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o [ 57%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o [ 58%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o [ 59%] Linking C static library ../../lib/libapbs_generic.a [ 59%] Built target apbs_generic Scanning dependencies of target apbs_mg [ 60%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o [ 61%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o [ 62%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o [ 63%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o [ 64%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o [ 65%] Linking C static library ../../lib/libapbs_mg.a [ 65%] Built target apbs_mg Scanning dependencies of target apbs [ 66%] Building C object src/CMakeFiles/apbs.dir/main.c.o [ 67%] Building C object src/CMakeFiles/apbs.dir/routines.c.o [ 68%] Linking C executable ../bin/apbs /usr/bin/ld: ../apbs/externals/fetk/maloc/lib/libmaloc.a(vio.c.o): in function Vio_ctor2': /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:769: undefined reference toxdrmem_create' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:767: undefined reference to xdrmem_create' /usr/bin/ld: ../apbs/externals/fetk/maloc/lib/libmaloc.a(vio.c.o): in functionVio_scanf': /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1499: undefined reference to xdr_double' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1451: undefined reference toxdr_string' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1461: undefined reference to xdr_char' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1470: undefined reference toxdr_int' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1488: undefined reference to xdr_float' /usr/bin/ld: ../apbs/externals/fetk/maloc/lib/libmaloc.a(vio.c.o): in functionVio_printf': /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1609: undefined reference to xdr_double' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1578: undefined reference toxdr_string' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1602: undefined reference to xdr_float' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1585: undefined reference toxdr_char' /usr/bin/ld: /mnt/usr/local/apbs-pdb2pqr/apbs/externals/fetk/maloc/src/vsys/vio.c:1590: undefined reference to `xdr_int' collect2: error: ld returned 1 exit status make[2]: [src/CMakeFiles/apbs.dir/build.make:108: bin/apbs] Error 1 make[1]: [CMakeFiles/Makefile2:298: src/CMakeFiles/apbs.dir/all] Error 2 make: *** [Makefile:130: all] Error 2

Il 2019-08-23 19:22 Juan ha scritto:

Hello @Vcald [1]! The build is failing because it's trying build against the RPC library and it doesn't seem to be on your LD path. Could you paste the output of the CMake configuration step? The CMake script checks if the library is present or not and shouldn't have included it if it wasn't present.

Could you please start on a fresh build folder. That is, make a new build folder and run the CMake and make commands there. Thanks!!

-- You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub [2], or mute the thread [3].

Links:

[1] https://github.com/Vcald [2] https://github.com/Electrostatics/apbs-pdb2pqr/issues/526?email_source=notifications&email_token=AMBMQW6J7VM2OY2OFQTY4OLQGAMFXA5CNFSM4IPBKOP2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5A2KXA#issuecomment-524395868 [3] https://github.com/notifications/unsubscribe-auth/AMBMQW34OHB2NC5T34CSUCTQGAMFXANCNFSM4IPBKOPQ

kozlac commented 4 years ago

Sorry for the delay, @Vcald. This one was little tricky but basically, what it comes down to is that Fedora removed some headers from the glibc standard library. So I have two options to build APBS in Fedora:

1) Disable XDR support by invoking cmake with the following option: $ cmake -DHAVE_RPC_RPC_H=FALSE <path to apbs/CMakeLists.txt> $ make 2) If you want XDR support: a. Install the libtirpc and libtirpc-devel libraries if you haven't already: $ sudo yum install libtirpc libtirpc-devel b. In the system folder /usr/include you will have two folders /usr/include/rpc and /usr/include/tirpc/rpc. Copy all the contents from /usr/include/tirpc/rpc into /usr/include/rpc. c. Copy the file /usr/include/tirpc/neconfig.h into /usr/include. d. In the file apbs/CMakeLists.txt look for the line that says: if(NOT WIN32) find_library(MATH_LIBRARY "m") list(APPEND APBS_LIB m stdc++)
endif()
And change the third line to: list (APPEND APBS_LIB m stdc++ tirpc) e. Now run cmake and make as you would normally and it should complete successfully: $ cmake <path to apbs/CMakeList.txt $ make

Any of those two options should be able to build APBS successfully. Please let me know if this solves your problem or if I can be of further assistance. Thanks!!

Vcald commented 4 years ago

Dear Juan, thank you very much...this solved the problem...I have indeed the same problem when compiling openbabel... What does rpc inclusion change in the program capabilities?

kozlac commented 4 years ago

I'm glad it worked @Vcald ! RPC (remote procedure call) allows for programs to call procedures in other address spaces (i.e. other computers). In our case, we are only using rpc's xdr.h part which allows us to encode data regardless of the operating system. I'm guessing openbabel might use it for similar reasons.