Error when Compiling HDF5 with Intel C/C++/Fortran compilers

[Jeb_b_]

Hi Everyone,

I'm getting this error when running make on HDF5 src with the intel compilers:

ld: warning: libimf.so, needed by ../src/.libs/libhdf5.so, not found (try using -rpath or -rpath-link)

ld: warning: libsvml.so, needed by ../src/.libs/libhdf5.so, not found (try using -rpath or -rpath-link)
ld: warning: libintlc.so.5, needed by ../src/.libs/libhdf5.so, not found (try using -rpath or -rpath-link)
ld: .libs/testhdf5: hidden symbol `__intel_cpu_indicator_init' in /export/el6/intel/2011.0.013/composerxe-2011.0.084/compiler/lib/intel64/libirc.a(cpu_disp.o) is referenced by DSO
ld: final link failed: Nonrepresentable section on output
make[1]: *** [testhdf5] Error 1
make[1]: Leaving directory `/home/[removed]/hdf5/hdf5-1.8.16/test'
make: *** [all-recursive] Error 1

any idea why I'm getting this?

[TimP]

It seems you don't have shared library path set.  Sourcing compilervars script would take care of this.

[Miriam_J_]

Hello,

Was this issue successfully solved by sourcing compilervars? I am getting *almost* the exact same error message as Jeb b. when running make on HDF5 with Intel compilers:

ld: warning: libimf.so, needed by ../src/.libs/libhdf5.so, not found (try using -rpath or -rpath-link)
ld: warning: libsvml.so, needed by ../src/.libs/libhdf5.so, not found (try using -rpath or -rpath-link)
ld: warning: libirng.so, needed by ../src/.libs/libhdf5.so, not found (try using -rpath or -rpath-link)
ld: warning: libintlc.so.5, needed by ../src/.libs/libhdf5.so, not found (try using -rpath or -rpath-link)
ld: .libs/testhdf5: hidden symbol `__intel_cpu_feature_

indicator_x' in /opt/intel/compilers_and_libraries_2016.1.150/linux/compiler/lib/intel64_lin/libirc.a(cpu_feature_disp.o) is referenced by DSO
ld: final link failed: Bad value
make[1]: *** [testhdf5] Error 1
make[1]: Leaving directory `/home/miriam/Downloads/hdf5-1.8.16/test'
make: *** [all-recursive] Error 1

I sourced compilervars using:

source <path>/compilervars.sh intel64

but I still receive the error.

I am on Ubuntu version 14.04, using Intel compiler 16.0.2. Thanks.

[luciana_V_]

I have the same problem.

Help please :(

libtool: link: warning: library `/home/alunos/Documentos/final01_04_16/szip/lib/libsz.la' was moved.
  CC       testhdf5.o
  CC       tarray.o
  CC       tattr.o
  CC       tchecksum.o
  CC       tconfig.o
  CC       tfile.o
  CC       tgenprop.o
  CC       th5o.o
  CC       th5s.o
  CC       tcoords.o
  CC       theap.o
  CC       tid.o
  CC       titerate.o
  CC       tmeta.o
  CC       tmisc.o
tmisc.c(2725): warning #810: conversion from "void *" to "const char" may lose significant bits
                          {"1234567", "1234567\0", "12345678", {NULL}};
                                                                ^

tmisc.c(2804): warning #810: conversion from "void *" to "const char" may lose significant bits
                          {"1234567", "1234567\0", "12345678", {NULL}};
                                                                ^

  CC       trefer.o
trefer.c(496): warning #69: integer conversion resulted in truncation
      hdset_reg_ref_t  nvrbuf[3]={{0},{101},{1000000000}}; /* buffer with non-valid refs */
                                             ^

  CC       trefstr.o
  CC       tselect.o
  CC       tskiplist.o
  CC       tsohm.o
  CC       ttime.o
  CC       ttst.o
  CC       tunicode.o
  CC       tvlstr.o
  CC       tvltypes.o
  CCLD     testhdf5
libtool: link: warning: library `/home/alunos/Documentos/final01_04_16/szip/lib/libsz.la' was moved.
libtool: link: warning: library `/home/alunos/Documentos/final01_04_16/szip/lib/libsz.la' was moved.
ld: warning: libimf.so, needed by ../src/.libs/libhdf5.so, not found (try using -rpath or -rpath-link)
ld: warning: libsvml.so, needed by ../src/.libs/libhdf5.so, not found (try using -rpath or -rpath-link)
ld: warning: libirng.so, needed by ../src/.libs/libhdf5.so, not found (try using -rpath or -rpath-link)
ld: warning: libintlc.so.5, needed by ../src/.libs/libhdf5.so, not found (try using -rpath or -rpath-link)
ld: .libs/testhdf5: hidden symbol `__intel_cpu_feature_indicator_x' in /opt/intel/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64_lin/libirc.a(cpu_feature_disp.o) is referenced by DSO
ld: final link failed: Bad value
Makefile:1519: recipe for target 'testhdf5' failed
make[1]: *** [testhdf5] Error 1

[Steven_L_Intel1]

These are C++ issues. I am moving this to the C++ forum.

[John_G_8]

I bet you upgraded to Xcode 7.3, which is responsible for this problem. This version of Xcode does not export variables to subshells as a security measure, so that setting the environment variable DYLD_LIBRARY_PATH to the appropriate location (like /opt/intel/lib) does not work. You have two choices, turn off SIP (not recommended) or hack the HDF5 build system to add the needed libraries explicitly. You will in fact need "-L/opt/intel/lib -lifport -lifcore -limf -lsvml -lintlc". You can check whether HDF5 provide a means to add these via configure.