AMBER Archive (2009)

Subject: Re: [AMBER] Installation issue

From: Ashveen Seenauth (ash2206_at_gmail.com)
Date: Tue Sep 22 2009 - 12:25:12 CDT

Oh okay, thanks Tom for this, this is what happens after entering "$
./configure_at -nobintraj gcc";

$ ./configure_at -nobintraj gcc
dirname: extra operand `Seenauth/amber10/src'
Try `dirname --help' for more information.
Setting AMBERHOME to

Warning: the X11 libraries are not in the usual location !
    To search for them try the command: locate libXt
    On Fedora Core 5 install an xorg-x11-devel package.
    On RedHat8 install an XFree86-devel package.
    For the moment Amber will be configured not to build XLEaP.

Testing the C compiler:
      gcc -DUSE_AMBER_C9XCOMPLEX -o testp testp.c
OK

Obtaining the C++ compiler version:
      g++ -v
The version is /managed/gcc-build/final-v3-bootstrap/gcc-3.4.4-999/configure
3.4.4
./configure_at: line 509: [: /managed/gcc-build/final-v3-bootstrap/gcc-3: intege
r expression expected
OK

Testing the g77 compiler:
     g77 -O2 -fno-automatic -finit-local-zero -o testp testp.f
OK

Testing flex:
OK

The configuration file, config.h, was successfully created.

The next step is to type 'make -f Makefile_at'

After this, I entered "export AMBERHOME=/home/name/amber10 (where name
is your name!)
 make -f Makefile_at" and the following takes place;

a - dsaupd.o
a - dsconv.o
a - dseigt.o
a - dsesrt.o
a - dseupd.o
a - dsgets.o
a - dsortc.o
a - dsortr.o
a - dstatn.o
a - dstats.o
a - dstqrb.o
a - dsarpack.o
a - wallclock.o
a - dmout.o
a - ivout.o
a - dvout.o
ranlib arpack.a
mv arpack.a /lib
make[1]: Leaving directory `/home/Ashveen Seenauth/amber10/src/carpack'
(cd clapack && make install )
make[1]: Entering directory `/home/Ashveen Seenauth/amber10/src/clapack'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
ar rv lapack.a dsyev.o dsyevd.o dormtr.o dormql.o dormqr.o dlansy.o dsytrd.o dor
gtr.o dsteqr.o dsterf.o dlascl.o dlamch.o ilaenv.o dlassq.o dsytd2.o dorm2l.o dl
atrd.o dorgql.o dorgqr.o dlasrt.o dlaset.o dlanst.o dlaev2.o dlasr.o dlapy2.o dl
artg.o dlae2.o dorg2r.o dlarft.o dlarfb.o dorg2l.o dlarfg.o dlarf.o dspev.o dlan
sp.o dsptrd.o dopgtr.o dposv.o dppsv.o dspsv.o dgeev.o dsptrs.o dsptrf.o dpptrs.
o dpptrf.o dgebak.o dtrevc.o dlacpy.o dhseqr.o dorghr.o dgehrd.o dgebal.o dlange
.o dlabad.o dlahqr.o dlarfx.o dlanhs.o dlaln2.o dgehd2.o dlahrd.o dlanv2.o dladi
v.o dgerq2.o dorm2r.o dlarnv.o dgeqr2.o dlaruv.o dspevd.o dstedc.o dopmtr.o dlae
d0.o dlaed1.o dlaed7.o dlaeda.o dlaed8.o dlaed9.o dlamrg.o dlaed2.o dlaed3.o dsy
gv.o dsygst.o dsygs2.o dlaed4.o dlaed5.o dlaed6.o dpotrf.o dpotrs.o dpotf2.o iee
eck.o dsyevd.o dormtr.o dormqr.o dormql.o dorm2l.o
ar: creating lapack.a
a - dsyev.o
a - dsyevd.o
a - dormtr.o
a - dormql.o
a - dormqr.o
a - dlansy.o
a - dsytrd.o
a - dorgtr.o
a - dsteqr.o
a - dsterf.o
a - dlascl.o
a - dlamch.o
a - ilaenv.o
a - dlassq.o
a - dsytd2.o
a - dorm2l.o
a - dlatrd.o
a - dorgql.o
a - dorgqr.o
a - dlasrt.o
a - dlaset.o
a - dlanst.o
a - dlaev2.o
a - dlasr.o
a - dlapy2.o
a - dlartg.o
a - dlae2.o
a - dorg2r.o
a - dlarft.o
a - dlarfb.o
a - dorg2l.o
a - dlarfg.o
a - dlarf.o
a - dspev.o
a - dlansp.o
a - dsptrd.o
a - dopgtr.o
a - dposv.o
a - dppsv.o
a - dspsv.o
a - dgeev.o
a - dsptrs.o
a - dsptrf.o
a - dpptrs.o
a - dpptrf.o
a - dgebak.o
a - dtrevc.o
a - dlacpy.o
a - dhseqr.o
a - dorghr.o
a - dgehrd.o
a - dgebal.o
a - dlange.o
a - dlabad.o
a - dlahqr.o
a - dlarfx.o
a - dlanhs.o
a - dlaln2.o
a - dgehd2.o
a - dlahrd.o
a - dlanv2.o
a - dladiv.o
a - dgerq2.o
a - dorm2r.o
a - dlarnv.o
a - dgeqr2.o
a - dlaruv.o
a - dspevd.o
a - dstedc.o
a - dopmtr.o
a - dlaed0.o
a - dlaed1.o
a - dlaed7.o
a - dlaeda.o
a - dlaed8.o
a - dlaed9.o
a - dlamrg.o
a - dlaed2.o
a - dlaed3.o
a - dsygv.o
a - dsygst.o
a - dsygs2.o
a - dlaed4.o
a - dlaed5.o
a - dlaed6.o
a - dpotrf.o
a - dpotrs.o
a - dpotf2.o
a - ieeeck.o
a - dsyevd.o
a - dormtr.o
a - dormqr.o
a - dormql.o
a - dorm2l.o
ranlib lapack.a
mv lapack.a /lib
make[1]: Leaving directory `/home/Ashveen Seenauth/amber10/src/clapack'
(cd cblas && make install )
make[1]: Entering directory `/home/Ashveen Seenauth/amber10/src/cblas'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
ar rv blas.a dasum.o daxpy.o dcopy.o ddot.o dgbmv.o dgemm.o dgemv.o dger.o dnrm2
.o drot.o drotg.o dsbmv.o dscal.o dspmv.o dspr.o dspr2.o dswap.o dsymm.o dsymv.o
 dsyr.o dsyr2.o dsyr2k.o dsyrk.o dtbmv.o dtbsv.o dtpmv.o dtpsv.o dtrmm.o dtrmv.o
 dtrsm.o dtrsv.o idamax.o lsame.o xerbla.o
ar: creating blas.a
a - dasum.o
a - daxpy.o
a - dcopy.o
a - ddot.o
a - dgbmv.o
a - dgemm.o
a - dgemv.o
a - dger.o
a - dnrm2.o
a - drot.o
a - drotg.o
a - dsbmv.o
a - dscal.o
a - dspmv.o
a - dspr.o
a - dspr2.o
a - dswap.o
a - dsymm.o
a - dsymv.o
a - dsyr.o
a - dsyr2.o
a - dsyr2k.o
a - dsyrk.o
a - dtbmv.o
a - dtbsv.o
a - dtpmv.o
a - dtpsv.o
a - dtrmm.o
a - dtrmv.o
a - dtrsm.o
a - dtrsv.o
a - idamax.o
a - lsame.o
a - xerbla.o
ranlib blas.a
mv blas.a /lib
make[1]: Leaving directory `/home/Ashveen Seenauth/amber10/src/cblas'
(cd f2c && make install )
make[1]: Entering directory `/home/Ashveen Seenauth/amber10/src/f2c'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
ar rv f2c.a abort_.o d_atan.o d_cosh.o d_int.o d_nint.o d_sinh.o d_abs.o
 d_atn2.o d_dim.o d_lg10.o d_prod.o d_sqrt.o exit_.o d_acos.o d_exp.o d
_log.o d_sign.o d_tan.o d_asin.o d_cos.o d_mod.o d_sin.o d_tanh.o wsfe
.o s_cmp.o s_copy.o s_paus.o s_rnge.o s_stop.o wsle.o xwsne.o util.o wref.o wrtf
mt.o rsne.o sfe.o sue.o uio.o open.o rdfmt.o rewind.o rsfe.o rsli.o ilnw.o inqui
re.o lread.o fmtlib.o ftell_.o iio.o err.o close.o dfe.o dolio.o due.o endfile.o
 backspace.o fmt.o sig_die.o pow_dd.o pow_di.o pow_ii.o lwrite.o i_len.o s_cat.o
 F77_aloc.o wsne.o typesize.o
ar: creating f2c.a
a - abort_.o
a - d_atan.o
a - d_cosh.o
a - d_int.o
a - d_nint.o
a - d_sinh.o
a - d_abs.o
a - d_atn2.o
a - d_dim.o
a - d_lg10.o
a - d_prod.o
a - d_sqrt.o
a - exit_.o
a - d_acos.o
a - d_exp.o
a - d_log.o
a - d_sign.o
a - d_tan.o
a - d_asin.o
a - d_cos.o
a - d_mod.o
a - d_sin.o
a - d_tanh.o
a - wsfe.o
a - s_cmp.o
a - s_copy.o
a - s_paus.o
a - s_rnge.o
a - s_stop.o
a - wsle.o
a - xwsne.o
a - util.o
a - wref.o
a - wrtfmt.o
a - rsne.o
a - sfe.o
a - sue.o
a - uio.o
a - open.o
a - rdfmt.o
a - rewind.o
a - rsfe.o
a - rsli.o
a - ilnw.o
a - inquire.o
a - lread.o
a - fmtlib.o
a - ftell_.o
a - iio.o
a - err.o
a - close.o
a - dfe.o
a - dolio.o
a - due.o
a - endfile.o
a - backspace.o
a - fmt.o
a - sig_die.o
a - pow_dd.o
a - pow_di.o
a - pow_ii.o
a - lwrite.o
a - i_len.o
a - s_cat.o
a - F77_aloc.o
a - wsne.o
a - typesize.o
ranlib f2c.a
mv f2c.a /lib
make[1]: Leaving directory `/home/Ashveen Seenauth/amber10/src/f2c'
(cd c9x-complex && make libmc.a )
make[1]: Entering directory `/home/Ashveen Seenauth/amber10/src/c9x-complex'
rm -f libmc.a
ar rv libmc.a cmplx.o clog.o cgamma.o stubs.o
ar: creating libmc.a
a - cmplx.o
a - clog.o
a - cgamma.o
a - stubs.o
ranlib libmc.a
mv libmc.a /lib
make[1]: Leaving directory `/home/Ashveen Seenauth/amber10/src/c9x-complex'
(cd cifparse && make install )
make[1]: Entering directory `/home/Ashveen Seenauth/amber10/src/cifparse'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
rm -f cifparse.a
ar rv cifparse.a lex.cif.o cifp.tab.o cifparse.o
ar: creating cifparse.a
a - lex.cif.o
a - cifp.tab.o
a - cifparse.o
ranlib cifparse.a
mv cifparse.a /lib
make[1]: Leaving directory `/home/Ashveen Seenauth/amber10/src/cifparse'
(cd nab && make install )
make[1]: Entering directory `/home/Ashveen Seenauth/amber10/src/nab'
(cd ../semantics; make)
make[2]: Entering directory `/home/Ashveen Seenauth/amber10/src/semantics'
./parse *.rules
./parse: can't read symbol file /dat/../src/nab/y.tab.h
make[2]: *** [checkexpr.c] Error 1
make[2]: Leaving directory `/home/Ashveen Seenauth/amber10/src/semantics'
make[1]: *** [checkexpr.c] Error 2
make[1]: Leaving directory `/home/Ashveen Seenauth/amber10/src/nab'
make: *** [install] Error 2

Hope this helps,
Ashveen

On Tue, Sep 22, 2009 at 11:55 AM, Tom Joseph <ttjoseph_at_gmail.com> wrote:
> He means that there were error messages printed before those last few
> lines that you didn't report. Please copy and paste more of the
> preceding output.
>
> --Tom
>
> 2009/9/22 Ashveen Seenauth <ash2206_at_gmail.com>:
>> Thank you for your reply Bill.
>>
>> But step 7 says;
>> # Once you are in the amber10/src directory, type the following:
>>
>> ./configure_at -nobintraj gcc
>>
>> [Aside: you can type "./configure_at -help" to see more options.]
>> Assuming(!) that this works, then type:
>>
>> export AMBERHOME=/home/name/amber10 (where name is your name!)
>> make -f Makefile_at
>>
>> At this point the screen will fill up with compilation messages, for
>> several minutes. The end you should see the message:
>>
>> "Completed installation of AmberTools ver. 1.1"
>>
>> [It's really version 1.2 -- we forgot to update the message when we
>> made the last revision :-( ]
>>
>> And after typing in "export AMBERHOME=/home/name/amber10 (where name
>> is your name!)", nothing happens but what do you mean to go back
>> further?
>>
>> Thanks,
>> Ashveen
>>
>> On Tue, Sep 22, 2009 at 11:31 AM, Bill Ross <ross_at_cgl.ucsf.edu> wrote:
>>> The actual error occurs before this final log - please go back further
>>> to find it.
>>>
>>> Bill
>>>
>>>> make[2]: *** [checkexpr.c] Error 1
>>>> make[2]: Leaving directory `/home/Ashveen Seenauth/amber10/src/semantics'
>>>> make[1]: *** [checkexpr.c] Error 2
>>>> make[1]: Leaving directory `/home/Ashveen Seenauth/amber10/src/nab'
>>>> make: *** [install] Error 2
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER_at_ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber