undefined reference to

[carlos.qu...@gmail.com]

Dear Plumed users, 

The following error occurred when install the Plumed program:

------------------------------------------------------------//------------------------------------------------------------

/home1/03137/tg824360/opt/lib/liblapack.a(dtrtri.f.o): In function `dtrtri_':

/home1/03137/tg824360/programs/lapack-3.5.0/SRC/dtrtri.f:(.text+0x1f5): undefined reference to `for_concat'

/home1/03137/tg824360/opt/lib/liblapack.a(ilaenv.f.o): In function `ilaenv_':

/home1/03137/tg824360/programs/lapack-3.5.0/SRC/ilaenv.f:(.text+0x11f): undefined reference to `for_cpystr'

/home1/03137/tg824360/opt/lib/liblapack.a(iparmq.f.o): In function `iparmq_':

/home1/03137/tg824360/programs/lapack-3.5.0/SRC/iparmq.f:(.text+0xd0): undefined reference to `f_lanint_val'

/home1/03137/tg824360/opt/lib/liblapack.a(xerbla.f.o): In function `xerbla_':

/home1/03137/tg824360/programs/lapack-3.5.0/SRC/xerbla.f:(.text+0x10): undefined reference to `for_len_trim'

/home1/03137/tg824360/programs/lapack-3.5.0/SRC/xerbla.f:(.text+0x55): undefined reference to `for_write_seq_fmt'

/home1/03137/tg824360/programs/lapack-3.5.0/SRC/xerbla.f:(.text+0x6e): undefined reference to `for_write_seq_fmt_xmit'

/home1/03137/tg824360/programs/lapack-3.5.0/SRC/xerbla.f:(.text+0x8b): undefined reference to `for_stop_core'

/home1/03137/tg824360/opt/lib/liblapack.a(dormtr.f.o): In function `dormtr_':

/home1/03137/tg824360/programs/lapack-3.5.0/SRC/dormtr.f:(.text+0x293): undefined reference to `for_concat'

/home1/03137/tg824360/programs/lapack-3.5.0/SRC/dormtr.f:(.text+0x360): undefined reference to `for_concat'

/home1/03137/tg824360/programs/lapack-3.5.0/SRC/dormtr.f:(.text+0x435): undefined reference to `for_concat'

/home1/03137/tg824360/programs/lapack-3.5.0/SRC/dormtr.f:(.text+0x502): undefined reference to `for_concat'

/home1/03137/tg824360/opt/lib/liblapack.a(dormql.f.o): In function `dormql_':

/home1/03137/tg824360/programs/lapack-3.5.0/SRC/dormql.f:(.text+0x235): undefined reference to `for_concat'

/home1/03137/tg824360/opt/lib/liblapack.a(dormql.f.o):/home1/03137/tg824360/programs/lapack-3.5.0/SRC/dormql.f:(.text+0x3a3): more undefined references to `for_concat' follow

/usr/bin/ld: link errors found, deleting executable `plumed'

make[5]: *** [plumed] Error 1

make[5]: Leaving directory `/home1/03137/tg824360/programs/plumed-2.0.2/src/lib'

make[4]: *** [all-static] Error 2

make[4]: Leaving directory `/home1/03137/tg824360/programs/plumed-2.0.2/src/lib'

make[3]: *** [all] Error 2

make[3]: Leaving directory `/home1/03137/tg824360/programs/plumed-2.0.2/src/lib'

make[2]: *** [lib] Error 2

make[2]: Leaving directory `/home1/03137/tg824360/programs/plumed-2.0.2/src'

make[1]: *** [lib] Error 2

make[1]: Leaving directory `/home1/03137/tg824360/programs/plumed-2.0.2'

make: *** [all] Error 2

------------------------------------------------------------//------------------------------------------------------------

In this case, i edited the makefile.conf to:

------------------------------------------------------------//------------------------------------------------------------

#CHECK_BOUNDARIES=-D_GLIBCXX_DEBUG

LIBS=-ldl

DYNAMIC_LIBS=-L/usr/lib -lstdc++ -L/<DIRECTORY OF LAPACK LIBRARY>/lib -llapack -L/<DIRECTORY OF LAPACK LIBRARY>/lib -lblas

DOUBLEPRECISION=-r8

CPPFLAGS=-D__PLUMED_HAS_DLOPEN $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE)

CXXFLAGS=-O -fPIC -Wall -wd981,383,1418

CFLAGS=-O -fPIC -Wall

LDFLAGS=-rdynamic

SOEXT=so

LDSO=icc -shared $(CFLAGS)

LD=icpc

LDF90=ifort

CXX=icpc

CC=icc

FC=ifort

GCCDEP=g++

------------------------------------------------------------//------------------------------------------------------------

Please, someone could help me solve this problem?

Thanks,

Carlos

[davide branduardi]

Hi!

It seems some problem coming from Lapack/Blas configuration.

I would try

1) Swap the Lapack/Blas ordering in the line DYNAMIC_LIBS library and check that they point to the right libraries and they are the right version (you should probably have a .so )

2) Redownload/Recompile Lapack+blas

D

[Giovanni Bussi]

Another possibility is that you have to add fortran libraries.

I assume you already read the manual and tried this:

"First of all, the DYNAMIC_LIB variable in the configuration file should contain the flag necessary to load these libraries (typically -llapack -lblas, in some case followed by -lgfortran but full path specification with -L should be necessary depending on your system configuration)."

Giovanni

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[carlos.qu...@gmail.com]

Hi,

Fist, thanks for suggestions. I did the procedure suggest by you and Davide, and occurred the same error. On the last try, i edited the following line of the Makefile.conf:

DYNAMIC_LIBS=-L/usr/lib64 -lstdc++ -lgfortran -L/home1/03137/tg824360/opt/lib -llapack -lblas

The Lapack/Blas libraries found in /home1/03137/tg824360/opt/lib are liblapack.a/libblas.a, and Fortran/std++ libraries found in /usr/lib64 are libgfortran.so.1, libgfortran.so.3, libstd++.so.5 and libstd++.so.6. According  to the manual, the problem would be solver with addition of -lgfortran flag. I also tried with 'SOEXT=' (in white), but no success. Any idea?

Thanks for help,

Carlos

[Giovanni Bussi]

Ask to your system administrator which flags are required to link lapack.

A possible alternative is to:

1. Switch to plumed 2.1

2. Use autoconf (./configure)

In this way if lapack/blas are not found an internal replacement will be used.

Giovanni

To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/ceb8bae0-5a09-4ed7-8b89-94ae5a470309%40googlegroups.com.

[carlos.qu...@gmail.com]

Hi Giovanni,

Many Many Many thanks for help. I asked to the system administrator which flags are required to link lapack, and he suggested use 'ifort' (option -mkl) for performance reasons. Now, the plumed program is worked.

Best,

Carlos