AMBER Archive (2009)

Subject: RE: [AMBER] Problem with amber9 installation

From: moitrayee_at_mbu.iisc.ernet.in
Date: Tue Jul 14 2009 - 02:02:39 CDT

Thanks a lot for the reply. I did a make clean when I get the following error,
the last few lines are as follows

/bin/rm: cannot remove `*.o': No such file or directory
make[1]: [clean] Error 1 (ignored)
/bin/rm *.mod
/bin/rm: cannot remove `*.mod': No such file or directory
make[1]: [clean] Error 1 (ignored)
make[1]: Leaving directory `/soft/amber9/src/build_amoeba'
cd netcdf/src; make clean
make[1]: Entering directory `/soft/amber9/src/netcdf/src'
Makefile:4: macros.make: No such file or directory
rules.make:118: warning: overriding commands for target `/'
Makefile:173: warning: ignoring old commands for target `/'
rules.make:120: warning: overriding commands for target `/'
rules.make:118: warning: ignoring old commands for target `/'
rules.make:122: warning: overriding commands for target `/'
rules.make:120: warning: ignoring old commands for target `/'
rules.make:124: warning: overriding commands for target `/'
rules.make:122: warning: ignoring old commands for target `/'
rules.make:127: warning: overriding commands for target `/'
rules.make:124: warning: ignoring old commands for target `/'
rules.make:130: warning: overriding commands for target `/'
rules.make:127: warning: ignoring old commands for target `/'
rules.make:145: warning: overriding commands for target `/man1'
rules.make:142: warning: ignoring old commands for target `/man1'
rules.make:147: warning: overriding commands for target `/man3'
rules.make:142: warning: ignoring old commands for target `/man3'
rules.make:150: warning: overriding commands for target `/man3f'
rules.make:142: warning: ignoring old commands for target `/man3f'
rules.make:154: warning: overriding commands for target `/man3f90'
rules.make:142: warning: ignoring old commands for target `/man3f90'
make[1]: *** No rule to make target `macros.make'. Stop.
make[1]: Leaving directory `/soft/amber9/src/netcdf/src'
make: [clean] Error 2 (ignored)
cd netcdf/lib && rm -f libnetcdf.a
/bin/sh: line 0: cd: netcdf/lib: No such file or directory
make: [clean] Error 1 (ignored)
cd netcdf/include && rm -f *.mod
/bin/sh: line 0: cd: netcdf/include: No such file or directory
make: [clean] Error 1 (ignored)

My .bashrc file is as follows:

# .bashrc

# User specific aliases and functions

# Source global definitions
if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi

export AMBERHOME=/soft/amber9
export PATH=$PATH:/soft/amber9/exe
export MKL_HOME=/opt/intel/mkl/8.0.2
export PATH=$PATH:/opt/intel/mkl/8.0.2/lib/32
export LD_LIBRARY_PATH=/opt/intel/mkl/8.0.2/lib/32
export LD_LIBRARY_PATH=/opt/intel/cmkl/10.0.1.014/lib/em64t
export PATH=$PATH:/opt/intel/cc/9.0/bin
export PATH=$PATH:/opt/intel/fc/9.0/bin
export PATH=$PATH:/opt/intel/fc/9.0/lib
source /opt/intel/fce/10.1.015/bin/ifortvars.sh

Best Regards,
Moitrayee

> Hi Moitrayee
>
> Did you do a make clean before the make? This looks to me like there was an
> old version of libdivcon.a there that has been built with an older compiler.
> Also do you have MKL_HOME defined / MKL installed?
>
> All the best
> Ross
>
>> -----Original Message-----
>> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
>> Behalf Of moitrayee_at_mbu.iisc.ernet.in
>> Sent: Monday, July 13, 2009 1:31 PM
>> To: amber_at_ambermd.org
>> Subject: [AMBER] Problem with amber9 installation
>>
>> Dear Amber Users,
>>
>> I am trying to install amber9 on a machine which has amber8 installed
>> already.
>> During make, I am getting a series of errors, the last few lines are as
>> below:
>>
>> ../dcqtp/src/qmmm/libdivcon.a(diislb.o): In function `diislb_':
>> ../obj/diislb.f:(.text+0x1fd9): undefined reference to `ddot_'
>> ../obj/diislb.f:(.text+0x2039): undefined reference to `daxpy_'
>> ../obj/diislb.f:(.text+0x2450): undefined reference to `ddot_'
>> ../obj/diislb.f:(.text+0x3881): undefined reference to `ddot_'
>> ../obj/diislb.f:(.text+0x38de): undefined reference to `daxpy_'
>> ../dcqtp/src/qmmm/libdivcon.a(prjfc.o): In function `prjfc_':
>> ../obj/prjfc.f:(.text+0x37b): undefined reference to `ddot_'
>> ../dcqtp/src/qmmm/libdivcon.a(math.o): In function `dgefa_':
>> ../obj/math.f:(.text+0xb7): undefined reference to `idamax_'
>> ../obj/math.f:(.text+0x159): undefined reference to `dscal_'
>> ../obj/math.f:(.text+0x22b): undefined reference to `daxpy_'
>> ../dcqtp/src/qmmm/libdivcon.a(math.o): In function `dgedi_':
>> ../obj/math.f:(.text+0x4b9): undefined reference to `dscal_'
>> ../obj/math.f:(.text+0x550): undefined reference to `daxpy_'
>> ../obj/math.f:(.text+0x942): undefined reference to `daxpy_'
>> ../obj/math.f:(.text+0x99d): undefined reference to `dswap_'
>> make[1]: *** [sander] Error 1
>> make[1]: Leaving directory `/soft/amber9/src/sander'
>> make: *** [serial] Error 2
>>
>> I am installing it serially on a fedora linux machine having 4GB ram
>> and core
>> two duo processor. I am using ifort to configure.
>> Any help would be of great benefit to me.
>>
>> Thanks in advance.
>> Best Regards,
>> Moitrayee
>>
>>
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