Hello:
Applied bugfixes 1-35 to ambertools 1.2/amber10. Then I had to abandon
intel/mkl of previous working compilation, moving to gcc and gfortran
version 4.3.2 in linux amd64. I have now commented out:
# Intel's MKL libraries for Amber and DOCK
# export MKL_HOME=/opt/intel/mkl/10.0.1.014/
# source $MKL_HOME/tools/environment/mklvarsem64t.sh
and libraries are:
francesco.tya64:~$ echo LD_LIBRARY_PATH
LD_LIBRARY_PATH
francesco.tya64:~$ echo $LD_LIBRARY_PATH
/opt/intel/cce/10.1.015/lib:/opt/intel/fce/10.1.015/lib:/opt/intel/cce/10.1.015/lib:/opt/intel/fce/10.1.015/lib:/usr/local/lib:/opt/acml4.2.0/gfortran64_mp_int64/lib:/usr/local/lib:/opt/acml4.2.0/gfortran64_mp_int64/lib
On these basis
# ./configure_amber gfortran
was successful, while
# make serial
reported errors
Configuring netcdf; (may be time-consuming)
NETCDF configure succeeded.
The configuration file, config_amber.h, was successfully created.
tya64:/usr/local/amber10/src# make serial
Starting installation of Amber10 (serial) at Fri Oct 1 18:07:41 CEST 2010.
cd lib && make install
make[1]: Entering directory `/usr/local/amber10/src/lib'
gfortran -o new2oldparm new2oldparm.o nxtsec.o
nxtsec.o: In function `nxtsec_':
_nxtsec.f:(.text+0x6a): undefined reference to `for_rewind'
_nxtsec.f:(.text+0xc0): undefined reference to `for_read_seq_fmt'
_nxtsec.f:(.text+0xf9): undefined reference to `for_cpstr'
_nxtsec.f:(.text+0x122): undefined reference to `for_f90_index'
_nxtsec.f:(.text+0x342): undefined reference to `for_read_int_fmt'
_nxtsec.f:(.text+0x363): undefined reference to `for_f90_index'
_nxtsec.f:(.text+0x568): undefined reference to `for_cpystr'
_nxtsec.f:(.text+0x6ab): undefined reference to `for_cpystr'
_nxtsec.f:(.text+0x705): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x73f): undefined reference to `for_write_seq_fmt_xmit'
_nxtsec.f:(.text+0x779): undefined reference to `for_write_seq_fmt_xmit'
_nxtsec.f:(.text+0x7d5): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x803): undefined reference to `for_cpystr'
_nxtsec.f:(.text+0x82c): undefined reference to `for_rewind'
_nxtsec.f:(.text+0x868): undefined reference to `for_rewind'
_nxtsec.f:(.text+0x8de): undefined reference to `for_read_seq_fmt'
_nxtsec.f:(.text+0x923): undefined reference to `for_cpstr'
_nxtsec.f:(.text+0xa92): undefined reference to `for_cpystr'
_nxtsec.f:(.text+0xac4): undefined reference to `for_rewind'
_nxtsec.f:(.text+0xb21): undefined reference to `for_cpystr'
_nxtsec.f:(.text+0xc26): undefined reference to `for_cpstr'
_nxtsec.f:(.text+0xd07): undefined reference to `for_read_seq_fmt'
_nxtsec.f:(.text+0xd4c): undefined reference to `for_cpstr'
_nxtsec.f:(.text+0xd9d): undefined reference to `for_rewind'
_nxtsec.f:(.text+0xdf3): undefined reference to `for_read_seq_fmt'
_nxtsec.f:(.text+0xe8a): undefined reference to `for_read_seq_fmt'
_nxtsec.f:(.text+0xecf): undefined reference to `for_cpstr'
_nxtsec.f:(.text+0xfcb): undefined reference to `for_cpystr'
_nxtsec.f:(.text+0x1075): undefined reference to `for_cpystr'
_nxtsec.f:(.text+0x10bf): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x10da): undefined reference to `for_stop_core'
_nxtsec.f:(.text+0x1113): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x112e): undefined reference to `for_stop_core'
_nxtsec.f:(.text+0x1167): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x1182): undefined reference to `for_stop_core'
_nxtsec.f:(.text+0x11bb): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x11d6): undefined reference to `for_stop_core'
_nxtsec.f:(.text+0x120f): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x122a): undefined reference to `for_stop_core'
_nxtsec.f:(.text+0x1263): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x127e): undefined reference to `for_stop_core'
_nxtsec.f:(.text+0x12b7): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x12d2): undefined reference to `for_stop_core'
_nxtsec.f:(.text+0x1356): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x1371): undefined reference to `for_stop_core'
_nxtsec.f:(.text+0x13f5): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x1410): undefined reference to `for_stop_core'
_nxtsec.f:(.text+0x1494): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x14af): undefined reference to `for_stop_core'
_nxtsec.f:(.text+0x1533): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x154e): undefined reference to `for_stop_core'
_nxtsec.f:(.text+0x15d2): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x15ed): undefined reference to `for_stop_core'
nxtsec.o: In function `nxtsec_crd_':
_nxtsec.f:(.text+0x176e): undefined reference to `for_rewind'
_nxtsec.f:(.text+0x17c4): undefined reference to `for_read_seq_fmt'
_nxtsec.f:(.text+0x17fd): undefined reference to `for_cpstr'
_nxtsec.f:(.text+0x1826): undefined reference to `for_f90_index'
_nxtsec.f:(.text+0x1a40): undefined reference to `for_read_int_fmt'
_nxtsec.f:(.text+0x1a61): undefined reference to `for_f90_index'
_nxtsec.f:(.text+0x1c60): undefined reference to `for_cpystr'
_nxtsec.f:(.text+0x1d9f): undefined reference to `for_cpystr'
_nxtsec.f:(.text+0x1df9): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x1e33): undefined reference to `for_write_seq_fmt_xmit'
_nxtsec.f:(.text+0x1e6d): undefined reference to `for_write_seq_fmt_xmit'
_nxtsec.f:(.text+0x1ec9): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x1ef7): undefined reference to `for_cpystr'
_nxtsec.f:(.text+0x1f20): undefined reference to `for_rewind'
_nxtsec.f:(.text+0x1f58): undefined reference to `for_rewind'
_nxtsec.f:(.text+0x1fce): undefined reference to `for_read_seq_fmt'
_nxtsec.f:(.text+0x2013): undefined reference to `for_cpstr'
_nxtsec.f:(.text+0x217e): undefined reference to `for_cpystr'
_nxtsec.f:(.text+0x21b0): undefined reference to `for_rewind'
_nxtsec.f:(.text+0x2207): undefined reference to `for_cpystr'
_nxtsec.f:(.text+0x230a): undefined reference to `for_cpstr'
_nxtsec.f:(.text+0x23eb): undefined reference to `for_read_seq_fmt'
_nxtsec.f:(.text+0x2430): undefined reference to `for_cpstr'
_nxtsec.f:(.text+0x2481): undefined reference to `for_rewind'
_nxtsec.f:(.text+0x24d7): undefined reference to `for_read_seq_fmt'
_nxtsec.f:(.text+0x256e): undefined reference to `for_read_seq_fmt'
_nxtsec.f:(.text+0x25b3): undefined reference to `for_cpstr'
_nxtsec.f:(.text+0x26ad): undefined reference to `for_cpystr'
_nxtsec.f:(.text+0x2757): undefined reference to `for_cpystr'
_nxtsec.f:(.text+0x27a1): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x27bc): undefined reference to `for_stop_core'
_nxtsec.f:(.text+0x27f5): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x2810): undefined reference to `for_stop_core'
_nxtsec.f:(.text+0x2849): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x2864): undefined reference to `for_stop_core'
_nxtsec.f:(.text+0x289d): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x28b8): undefined reference to `for_stop_core'
_nxtsec.f:(.text+0x28f1): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x290c): undefined reference to `for_stop_core'
_nxtsec.f:(.text+0x2945): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x2960): undefined reference to `for_stop_core'
_nxtsec.f:(.text+0x2999): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x29b4): undefined reference to `for_stop_core'
_nxtsec.f:(.text+0x2a38): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x2a53): undefined reference to `for_stop_core'
_nxtsec.f:(.text+0x2ad7): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x2af2): undefined reference to `for_stop_core'
_nxtsec.f:(.text+0x2b76): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x2b91): undefined reference to `for_stop_core'
_nxtsec.f:(.text+0x2c15): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x2c30): undefined reference to `for_stop_core'
_nxtsec.f:(.text+0x2cb4): undefined reference to `for_write_seq_fmt'
_nxtsec.f:(.text+0x2ccf): undefined reference to `for_stop_core'
collect2: ld returned 1 exit status
make[1]: *** [new2oldparm] Error 1
make[1]: Leaving directory `/usr/local/amber10/src/lib'
make: *** [serial] Error 2
tya64:/usr/local/amber10/src#
I am confused about what to do now. Thanks for suggestions
francesco pietra
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Received on Fri Oct 01 2010 - 09:30:03 PDT
