cannot find -lcr Rosetta3.5 installation

[Anonymous]

Dear ‘Rosettaers’,
I’d tried to compile the Rosetta3.5 on my Server[1] and I couldn’t. I tried to compile Rosetta using this command: scons bin mode=release -j 24 extras=mpi,static cxx_ver=4.6 cxx=gcc After a few minutes of compilation the error came and it is following:
mpiCC -o build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/InterfaceAnalyzer.mpistatic.linuxgccrelease -static build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/apps/public/analysis/InterfaceAnalyzer.o -Lexternal/lib -Lbuild/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static -Lsrc -Lbuild/external/release/linux/3.13/64/x86/gcc/4.6/mpi-static -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.7 -lprotocols.6 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols_h.4 -lprotocols_g.4 -lprotocols_f.4 -lprotocols_e.4 -lprotocols_d.4 -lprotocols_c.4 -lprotocols_b.4 -lprotocols_a.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lcppdb -lsqlite3
/usr/bin/ld: cannot find -lcr
/usr/lib/x86_64-linux-gnu/libmpich.a(tcp_init.o): In function `MPID_nem_tcp_get_business_card’:
(.text+0x453): warning: Using ‘gethostbyname’ in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
collect2: error: ld returned 1 exit status
/usr//bin/ld:usr /cannotbin /findld :- lcrcannot
/findusr /-liblcr/
x86_64/-usrlinux/-libgnu//x86_64libmpich.a-(linuxtcp_init.o-)gnu:/ libmpich.aIn( tcp_init.ofunction) :` MPID_nem_tcp_get_business_cardIn’ :function
(`.MPID_nem_tcp_get_business_cardtext’+:0x453
)(:. textwarning+:0x453 )Using: ‘warninggethostbyname:’ Usingin ‘staticallygethostbyname ‘linked inapplications staticallyrequires linkedat applicationsruntime requiresthe atshared runtimelibraries thefrom sharedthe librariesglibc fromversion theused glibcfor versionlinking
used for linking
collect2: error: ld returned 1 exit status
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/swa_rna_util.mpistatic.linuxgccrelease] Error 1
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/swa_rna_analytical_closure.mpistatic.linuxgccrelease] Error 1
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/rna_database.mpistatic.linuxgccrelease] Error 1
collect2: error: ld terminated with signal 9 [Killed]
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/AnchoredDesign.mpistatic.linuxgccrelease] Error 1
collect2: error: ld terminated with signal 9 [Killed]
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/oop_design.mpistatic.linuxgccrelease] Error 1
collect2: error: ld terminated with signal 9 [Killed]
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/UBQ_E2_thioester.mpistatic.linuxgccrelease] Error 1
collect2: error: ld terminated with signal 9 [Killed]
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/vip.mpistatic.linuxgccrelease] Error 1
collect2: error: ld terminated with signal 9 [Killed]
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/ddg_monomer.mpistatic.linuxgccrelease] Error 1
collect2: error: ld terminated with signal 9 [Killed]
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/fast_clustering.mpistatic.linuxgccrelease] Error 1
collect2: error: ld terminated with signal 9 [Killed]
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/UBQ_Gp_LYX-Cterm.mpistatic.linuxgccrelease] Error 1
collect2: error: ld terminated with signal 9 [Killed]
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/rotamer_recovery.mpistatic.linuxgccrelease] Error 1
collect2: error: ld terminated with signal 9 [Killed]
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/idealize_jd2.mpistatic.linuxgccrelease] Error 1
collect2: error: ld terminated with signal 9 [Killed]
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/gen_apo_grids.mpistatic.linuxgccrelease] Error 1
collect2: error: ld terminated with signal 9 [Killed]
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/packstat.mpistatic.linuxgccrelease] Error 1
collect2: error: ld terminated with signal 9 [Killed]
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/InterfaceAnalyzer.mpistatic.linuxgccrelease] Error 1
collect2: error: ld terminated with signal 9 [Killed]
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/design_contrast_and_statistic.mpistatic.linuxgccrelease] Error 1
collect2: error: ld terminated with signal 9 [Killed]
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/extract_pdbs.mpistatic.linuxgccrelease] Error 1
/usr/bin/ld: cannot find -lcr
/usr/lib/x86_64-linux-gnu/libmpich.a(tcp_init.o): In function `MPID_nem_tcp_get_business_card’:
(.text+0x453): warning: Using ‘gethostbyname’ in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
collect2: error: ld returned 1 exit status
/usr/bin/ld: cannot find -lcr
/usr/lib/x86_64-linux-gnu/libmpich.a(tcp_init.o): In function `MPID_nem_tcp_get_business_card’:
(.text+0x453): warning: Using ‘gethostbyname’ in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
collect2: error: ld returned 1 exit status
/usr/bin/ld: cannot find -lcr
/usr/lib/x86_64-linux-gnu/libmpich.a(tcp_init.o): In function `MPID_nem_tcp_get_business_card’:
(.text+0x453): warning: Using ‘gethostbyname’ in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
collect2: error: ld returned 1 exit status
/usr/bin/ld: cannot find -lcr
/usr/lib/x86_64-linux-gnu/libmpich.a(tcp_init.o): In function `MPID_nem_tcp_get_business_card’:
(.text+0x453): warning: Using ‘gethostbyname’ in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
collect2: error: ld returned 1 exit status
/usr//bin/ldusr: cannot/bin find/ld -: lcr
cannot find -lcr/
/usr/usr/liblib//x86_64x86_64–linuxlinux–gnugnu//libmpich.alibmpich.a((tcp_init.otcp_init.o)):: InIn functionfunction `MPID_nem_tcp_get_business_card`MPID_nem_tcp_get_business_card’:
‘.
(text+.text0x453)+0x453: ):warning: warning Using: Using ‘gethostbyname ” gethostbyname’in instatically staticallylinked linkedapplications applicationsrequires requiresat atruntime runtimethe theshared sharedlibraries librariesfrom fromthe theglibc glibcversion versionused usedfor forlinking
linking
collect2: error: ld returned 1 exit status
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/rosettaDNA.mpistatic.linuxgccrelease] Error 1
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/ligand_rpkmin.mpistatic.linuxgccrelease] Error 1
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/membrane_abinitio2.mpistatic.linuxgccrelease] Error 1
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/gen_lig_grids.mpistatic.linuxgccrelease] Error 1
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/extract_atomtree_diffs.mpistatic.linuxgccrelease] Error 1
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/docking_protocol.mpistatic.linuxgccrelease] Error 1
/usr/bin/ld: cannot find -lcr
/usr/lib/x86_64-linux-gnu/libmpich.a(tcp_init.o): In function `MPID_nem_tcp_get_business_card’:
(.text+0x453): warning: Using ‘gethostbyname’ in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.6/mpi-static/score_jd2.mpistatic.linuxgccrelease] Error 1
scons: building terminated because of errors.

I presume that this error was due to my SO (Ubuntu 14.04.1) doesn’t find this library (lcr) when compiling Rosetta3.5. I’ve been searching some tips about how to resolve this error and I found one at this post: http://lammps.sandia.gov/threads/msg22091.html. It advises me about the instaIlation of libcr-dev and I’d did it (sudo apt-get install libcr-dev;libcr-dev is already the newest version.) and I tried once to compile Rosetta.
As the compilation failed again and I’d installed libcr [2,3], I wonder to know how can I solve this problem and compile Rosettta using MPI [4] on my 24 cpu?
Regards.

[1] Server details
SO:Ubuntu 14.04.1 LTS
Linux labimm-115 3.13.0-45-generic #74-Ubuntu SMP Tue Jan 13 19:36:28 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
Architecture: x86_64
CPU(s): 24, Vendor ID: GenuineIntel
CPU op-mode(s): 32-bit, 64-bit

[2] locate libcr
/lib/libcryptsetup.so.4
/lib/libcryptsetup.so.4.5.0
/lib/modules/3.13.0-45-generic/kernel/lib/libcrc32c.ko
/lib/modules/3.2.0-58-generic/kernel/lib/libcrc32c.ko
/lib/x86_64-linux-gnu/libcrypt-2.19.so
/lib/x86_64-linux-gnu/libcrypt.so.1
/lib/x86_64-linux-gnu/libcrypto.so.1.0.0
/lib32/libcrypt-2.19.so
/lib32/libcrypt.so.1
/usr/include/libcr.h
/usr/lib/libcr.la
/usr/lib/libcr.so
/usr/lib/libcr.so.0
/usr/lib/libcr.so.0.5.5
/usr/lib/libcr_omit.la
/usr/lib/libcr_omit.so
/usr/lib/libcr_omit.so.0
/usr/lib/libcr_omit.so.0.5.5
/usr/lib/libcr_run.la
/usr/lib/libcr_run.so
/usr/lib/libcr_run.so.0
/usr/lib/libcr_run.so.0.5.5
/usr/lib/chromium-browser/libs/libcrcrypto.so
/usr/lib/chromium-browser/libs/libcrssl.so
/usr/lib/debug/lib/x86_64-linux-gnu/libcrypt-2.19.so
/usr/lib/x86_64-linux-gnu/libcrack.so.2
/usr/lib/x86_64-linux-gnu/libcrack.so.2.9.0
/usr/lib/x86_64-linux-gnu/libcroco-0.6.so.3
/usr/lib/x86_64-linux-gnu/libcroco-0.6.so.3.0.1
/usr/lib/x86_64-linux-gnu/libcrypt.a
/usr/lib/x86_64-linux-gnu/libcrypt.so
/usr/lib/x86_64-linux-gnu/gtk-2.0/2.10.0/engines/libcrux-engine.so
/usr/lib/x86_64-linux-gnu/sasl2/libcrammd5.so
/usr/lib/x86_64-linux-gnu/sasl2/libcrammd5.so.2
/usr/lib/x86_64-linux-gnu/sasl2/libcrammd5.so.2.0.25
/usr/lib/x86_64-linux-gnu/unity-control-center-1/panels/libcredentials.so
/usr/share/doc/libcr-dev
/usr/share/doc/libcr0
/usr/share/doc/libcrack2
/usr/share/doc/libcroco3
/usr/share/doc/libcrypt-passwdmd5-perl
/usr/share/doc/libcryptsetup4
/usr/share/doc/libcr-dev/changelog.Debian.gz
/usr/share/doc/libcr-dev/copyright
/usr/share/doc/libcr-dev/counting.c
/usr/share/doc/libcr-dev/file_counting.c
/usr/share/doc/libcr-dev/io_bench.c.gz
/usr/share/doc/libcr-dev/pipe_counting.c
/usr/share/doc/libcr-dev/pthread_counting.c
/usr/share/doc/libcr-dev/pthread_misc.c.gz
/usr/share/doc/libcr0/changelog.Debian.gz
/usr/share/doc/libcr0/copyright
/usr/share/doc/libcrack2/README.gz
/usr/share/doc/libcrack2/changelog.Debian.gz
/usr/share/doc/libcrack2/copyright
/usr/share/doc/libcrack2/libcrack2.html
/usr/share/doc/libcroco3/AUTHORS
/usr/share/doc/libcroco3/NEWS.gz
/usr/share/doc/libcroco3/README
/usr/share/doc/libcroco3/TODO
/usr/share/doc/libcroco3/changelog.Debian.gz
/usr/share/doc/libcroco3/copyright
/usr/share/doc/libcrypt-passwdmd5-perl/README
/usr/share/doc/libcrypt-passwdmd5-perl/changelog.Debian.gz
/usr/share/doc/libcrypt-passwdmd5-perl/copyright
/usr/share/doc/libcryptsetup4/NEWS.Debian.gz
/usr/share/doc/libcryptsetup4/changelog.Debian.gz
/usr/share/doc/libcryptsetup4/copyright
/usr/share/doc-base/libcrack2
/usr/src/linux-headers-3.13.0-45-generic/include/config/libcrc32c.h
/var/lib/doc-base/documents/libcrack2
/var/lib/doc-base/omf/libcrack2
/var/lib/doc-base/omf/libcrack2/libcrack2-C.omf
/var/lib/dpkg/info/libcr-dev.list
/var/lib/dpkg/info/libcr-dev.md5sums
/var/lib/dpkg/info/libcr0.list
/var/lib/dpkg/info/libcr0.md5sums
/var/lib/dpkg/info/libcr0.postinst
/var/lib/dpkg/info/libcr0.postrm
/var/lib/dpkg/info/libcr0.shlibs
/var/lib/dpkg/info/libcr0.symbols
/var/lib/dpkg/info/libcrack2:amd64.list
/var/lib/dpkg/info/libcrack2:amd64.md5sums
/var/lib/dpkg/info/libcrack2:amd64.postinst
/var/lib/dpkg/info/libcrack2:amd64.postrm
/var/lib/dpkg/info/libcrack2:amd64.shlibs
/var/lib/dpkg/info/libcrack2:amd64.symbols
/var/lib/dpkg/info/libcroco3:amd64.list
/var/lib/dpkg/info/libcroco3:amd64.md5sums
/var/lib/dpkg/info/libcroco3:amd64.postinst
/var/lib/dpkg/info/libcroco3:amd64.postrm
/var/lib/dpkg/info/libcroco3:amd64.shlibs
/var/lib/dpkg/info/libcroco3:amd64.symbols
/var/lib/dpkg/info/libcrypt-passwdmd5-perl.list
/var/lib/dpkg/info/libcrypt-passwdmd5-perl.md5sums
/var/lib/dpkg/info/libcryptsetup4.list
/var/lib/dpkg/info/libcryptsetup4.md5sums
/var/lib/dpkg/info/libcryptsetup4.postinst
/var/lib/dpkg/info/libcryptsetup4.postrm
/var/lib/dpkg/info/libcryptsetup4.shlibs
/var/lib/dpkg/info/libcryptsetup4.symbols

[3]locate libcr-dev
/usr/share/doc/libcr-dev
/usr/share/doc/libcr-dev/changelog.Debian.gz
/usr/share/doc/libcr-dev/copyright
/usr/share/doc/libcr-dev/counting.c
/usr/share/doc/libcr-dev/file_counting.c
/usr/share/doc/libcr-dev/io_bench.c.gz
/usr/share/doc/libcr-dev/pipe_counting.c
/usr/share/doc/libcr-dev/pthread_counting.c
/usr/share/doc/libcr-dev/pthread_misc.c.gz
/var/lib/dpkg/info/libcr-dev.list
/var/lib/dpkg/info/libcr-dev.md5sums

[4] mpichversion
MPICH Version: 3.0.4
MPICH Release date: Wed Apr 24 10:08:10 CDT 2013
MPICH Device: ch3:nemesis
MPICH configure: –build=x86_64-linux-gnu –prefix=/usr –includedir=${prefix}/include –mandir=${prefix}/share/man –infodir=${prefix}/share/info –sysconfdir=/etc –localstatedir=/var –libdir=${prefix}/lib/x86_64-linux-gnu –libexecdir=${prefix}/lib/x86_64-linux-gnu –disable-maintainer-mode –disable-dependency-tracking –enable-shared –prefix=/usr –enable-fc –disable-rpath –disable-wrapper-rpath –sysconfdir=/etc/mpich –libdir=/usr/lib/x86_64-linux-gnu –includedir=/usr/include/mpich –docdir=/usr/share/doc/mpich –with-hwloc-prefix=system –enable-checkpointing –with-hydra-ckpointlib=blcr
MPICH CC: cc -g -O2 -fstack-protector –param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector –param=ssp-buffer-size=4 -Wformat -Werror=format-security -O2
MPICH CXX: c++ -g -O2 -fstack-protector –param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector –param=ssp-buffer-size=4 -Wformat -Werror=format-security -O2
MPICH F77: gfortran -g -O2 -g -O2 -O2
MPICH FC: gfortran -g -O2 -O2

[Anonymous]

Which, if any, of the other builds work? In particular, do you need static? I have a feeling that A) this is a library that the underlying MPI code needs, not something Rosetta directly requires (certainly I’ve never heard of it), and it might be that you have the dynamically-linkable library but not the static. If this is one 24-core system, the static build is probably less efficient than the dynamic build anyway (independent copies of libraries in memory).

[Anonymous]

Thanks SMLewis,
I’ve just finished to compile Rosetta3.5 with MPI on 24 cpus using the dynamic library.
Cheers.

[Author]

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