Re: [AMBER] compilation with gcc 4.5.1 under openSuSE 11.4 64-bits

From: JORGE IULEK <jiulek.ig.com.br>
Date: Wed, 25 May 2011 16:09:08 -0300

Thanks Dr. Case for your initial help.

> On Wed, May 25, 2011, JORGE IULEK wrote:
>> I recently noved to a new laptop (where I calculate energies after
>> cluster productive runs). In my former laptop, I had openSuSE 11.2 (64
>> bits), to which I compiled AmberTools 1.3 and Amber10, gcc version 4.4(.1
as
>> reported by configure)-4.2, all patches applied, following instructions
at
>> http://archive.ambermd.org/201001/0150.html, and things ran as expected.
To
>> my new laptop, I went to openSuSE 11.4 (64 bits), gcc is 4.5(.1 as
reported
>> by configure)-19.1 (as reported by yast2). AmberTools compilation seems
to
>> go fine, but at "test" I get the error:
> As a workaround, edit the $AMBERHOME/test/nab/Makefile to skip the duplex
> test. See if anything else is broken.
>
    I took out duplex_test from the line:

" test: duplex_test reflexive_test hashed_test shifts_test sff_test \"

*and* also cut out

"
duplex_test::
    .echo =====================================================
    .echo "Running test to make dna duplex: "
    .echo
    .$(BINDIR)/nab $(NABFLAGS) -o duplex$(SFX) duplex.nab; \
        ./duplex$(SFX) < duplex.in
    .-diff d01.pdb.check d01.pdb && ( echo " PASSED"; rm -f d01.pdb ) \
        || echo " FAILED (possibly: see if diffs above look OK)"
    .-rm -f duplex$(SFX) d01.lin duplex.c
"


    From Makefile (I notice there is "deform_test" right after
"duplex_test", which is not called (?) in the "test:" line), and the result
(from which I snipped some lines I think are irrelevant) was:


"
(find antechamber -name '*.out' -o -name '*.log' -o -name '*.lib' -o \
        -name "*.dif" | \
while read dif ;\
do \
    rm -f $dif ;\
done ;\
)
(cd leap && /bin/rm -f *.log *.out *.lib *.top )
(cd ptraj_rmsa && /bin/rm -f *.dif )
(cd ptraj_matrix && /bin/rm -f *.dif )
(cd ptraj_rms && /bin/rm -f *.dif )
(cd ptraj_les && /bin/rm -f *.dif )
(find sleap -name '*.out' -o -name '*.log' -o -name '*.lib' -o \
        -name "*.dif" | \
while read dif ;\
do \
    rm -f $dif ;\
done ;\
)
/bin/rm -f TEST_FAILURES.diff
( cd nab; make test )
make[1]: Entering directory `/usr/local/amber11/test/nab'
=====================================================
Running Reflexive test:

1,52c1,52
< i = 0
[snipped]
< 1.000000
< hi mom!
< 4.000 4.000 4.000
< 1.000 1.000 1.000

---
> i = %
> ni = %
[snipped]
> n%
> n   4.000    4.000    4.000
>
1.000000    1.000 1.000000000000000000000000000000000
    FAILED (possibly: see if diffs above look OK)
=====================================================
Running test of hashed arrays:
1,52c1,53
<  51 {
<  50 static
[snipped]
> n 36 %
> n
\ No newline at end of file
    FAILED
=====================================================
Running test to compute chemical shifts
   (This tests many parts of the compiler and libraries)
2c2
< Reading observed shifts from 5pti.obs
---
> Getting coodiinates from5pti.dbbs
4,320d3
< # BPTI CHEMICAL SHIFTS pH 4.6 36C
[snipped]
< T:ALA:58:HB3         -0.011     0.073    -0.080    -0.041    -0.058
-0.110
   FAILED (possibly: see if diffs above look OK)
=====================================================
Running test to do simple minimization
   (This tests the molecular mechanics interface)
getpdb: can't open file 2.ddb
make[1]: *** [sff_test] Error 1
make[1]: Leaving directory `/usr/local/amber11/test/nab'
make: *** [test.nab] Error 2
"
    So I ask whether there should be something more to test.
    About the other route:
> Otherwise, download AmberTools 1.5 into an amber11 tree, and set your
AMBERHOME
> variable to that location.  You can use that version of NAB (and other
amber
> tools), and continue to use the sander or pmemd programs from the Amber10
> directory tree.
./configure gnu
gave the error:
"
Checking for libbz2: testp.c:2:19: fatal error: bzlib.h: No such file or
directory
compilation terminated.
./configure: line 1641: ./testp: No such file or directory
Not found.
"
    but I have the (linux) libbz2 package (64-bits, not 32-bits) installed.
    In spite of that I went to make install and it finished.
    So I installed amber10 as described before, confifgure, make serial,
fine, but at test I get:
"
cd rdc && ./Run.dip
  ./Run.dip:  Program error
make: *** [test.sander.BASIC] Error 1
"
Jorge
> ...good luck...dac
>
>
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Received on Wed May 25 2011 - 12:30:03 PDT