AMBER Archive (2009)

Subject: Re: [AMBER] Installation issue

From: Tom Joseph (ttjoseph_at_gmail.com)
Date: Tue Sep 22 2009 - 12:41:51 CDT

I think the AMBER build process doesn't like that your home directory
name includes a space (between your first and last names). Try
building AMBER from a directory whose absolute path does not include a
space.

--Tom

2009/9/22 Ashveen Seenauth <ash2206_at_gmail.com>:
> 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
>>>>
>>>> _______________________________________________
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>> _______________________________________________
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>>>
>>
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>>
>
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