Hi,
So I have found a few solutions to problems compiling amber10 in the mailing archives but was unable to find this particular solution. I am running ubuntu 9.04 and am trying to compile amber10 with no flags and gfortran as the compiler.
Ambertools was successful but amber 10 was not. Here is what the terminal output looks like right when i get the error.
make[1]: Entering directory `/usr/local/bin/amber10/src/etc'
cd ../lib ; ./Makelist ../lib/amopen.o ../lib/mexit.o ../lib/nxtsec.o
make[2]: Entering directory `/usr/local/bin/amber10/src/lib'
make[2]: `amopen.o' is up to date.
make[2]: Leaving directory `/usr/local/bin/amber10/src/lib'
make[2]: Entering directory `/usr/local/bin/amber10/src/lib'
make[2]: `mexit.o' is up to date.
make[2]: Leaving directory `/usr/local/bin/amber10/src/lib'
make[2]: Entering directory `/usr/local/bin/amber10/src/lib'
make[2]: `nxtsec.o' is up to date.
make[2]: Leaving directory `/usr/local/bin/amber10/src/lib'
gfortran -o ambpdb ambpdb.o forFIRSTtype.o forFIRSTbond.o forFIRSThbond.o forFIRSTteth.o forFIRSToutp.o forFIRSTsugar.o ../lib/amopen.o ../lib/mexit.o ../lib/nxtsec.o
gfortran -o nucgen nucgen.o ngfil.o ../lib/amopen.o ../lib/mexit.o ../lib/nxtsec.o
g++ -c -DBINTRAJ -I../netcdf/include -o elsize.o elsize.cc
elsize.cc: In function ‘int main(int, char**)’:
elsize.cc:117: error: ‘exit’ was not declared in this scope
elsize.cc:124: error: ‘strcmp’ was not declared in this scope
elsize.cc:145: error: ‘strcmp’ was not declared in this scope
elsize.cc:160: error: ‘calloc’ was not declared in this scope
elsize.cc:171: error: ‘exit’ was not declared in this scope
elsize.cc:233: error: ‘exit’ was not declared in this scope
elsize.cc:295: error: ‘exit’ was not declared in this scope
elsize.cc:339: error: ‘exit’ was not declared in this scope
elsize.cc: In function ‘atom_count GetNumberOfAtoms(const char*, int)’:
elsize.cc:504: error: ‘exit’ was not declared in this scope
elsize.cc: In function ‘atom_count ReadAtomicCoordinates(const char*, int, atom_count, double*, double*, double*, double*, double*)’:
elsize.cc:565: error: ‘exit’ was not declared in this scope
make[1]: *** [elsize.o] Error 1
make[1]: Leaving directory `/usr/local/bin/amber10/src/etc'
make: *** [serial] Error 2
If I run the make test, mostly everything passes up until this point:
cd pbsa_dmp && ./Run.dmp.min
diffing mdout.dmp.min.save with mdout.dmp.min
PASSED
==============================================================
cd pbsa_pgb && ./Run.pbpgb.min
diffing mdout.pbpgb.min.save with mdout.pbpgb.min
PASSED
==============================================================
cd pbsa_radi && ./Run.ion.min
diffing ./out.save/Li.out.save with Li.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check Li.out.dif
==============================================================
diffing ./out.save/Na.out.save with Na.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check Na.out.dif
==============================================================
diffing ./out.save/K.out.save with K.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check K.out.dif
==============================================================
diffing ./out.save/Rb.out.save with Rb.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check Rb.out.dif
==============================================================
diffing ./out.save/Cs.out.save with Cs.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check Cs.out.dif
==============================================================
diffing ./out.save/F.out.save with F.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check F.out.dif
==============================================================
diffing ./out.save/Cl.out.save with Cl.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check Cl.out.dif
==============================================================
diffing ./out.save/IM.out.save with IM.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check IM.out.dif
==============================================================
diffing ./out.save/Br.out.save with Br.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check Br.out.dif
==============================================================
diffing ./out.save/I.out.save with I.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check I.out.dif
==============================================================
diffing ./out.save/MG.out.save with MG.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check MG.out.dif
==============================================================
diffing ./out.save/Ca.out.save with Ca.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check Ca.out.dif
==============================================================
diffing ./out.save/Zn.out.save with Zn.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check Zn.out.dif
==============================================================
diffing ./out.save/tp3.out.save with tp3.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check tp3.out.dif
==============================================================
diffing ./out.save/ile.out.save with ile.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check ile.out.dif
==============================================================
diffing ./out.save/leu.out.save with leu.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check leu.out.dif
==============================================================
diffing ./out.save/val.out.save with val.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check val.out.dif
==============================================================
diffing ./out.save/phe.out.save with phe.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check phe.out.dif
==============================================================
diffing ./out.save/trp.out.save with trp.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check trp.out.dif
==============================================================
diffing ./out.save/hid.out.save with hid.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check hid.out.dif
==============================================================
diffing ./out.save/hie.out.save with hie.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check hie.out.dif
==============================================================
diffing ./out.save/nhe.out.save with nhe.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check nhe.out.dif
==============================================================
diffing ./out.save/tyr.out.save with tyr.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check tyr.out.dif
==============================================================
diffing ./out.save/ser.out.save with ser.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check ser.out.dif
==============================================================
diffing ./out.save/thr.out.save with thr.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check thr.out.dif
==============================================================
diffing ./out.save/cys.out.save with cys.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check cys.out.dif
==============================================================
diffing ./out.save/cyx.out.save with cyx.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check cyx.out.dif
==============================================================
diffing ./out.save/met.out.save with met.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check met.out.dif
==============================================================
diffing ./out.save/lyn.out.save with lyn.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check lyn.out.dif
==============================================================
diffing ./out.save/ash.out.save with ash.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check ash.out.dif
==============================================================
diffing ./out.save/glh.out.save with glh.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check glh.out.dif
==============================================================
diffing ./out.save/asn.out.save with asn.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check asn.out.dif
==============================================================
diffing ./out.save/gln.out.save with gln.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check gln.out.dif
==============================================================
diffing ./out.save/nma.out.save with nma.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check nma.out.dif
==============================================================
diffing ./out.save/alabk.out.save with alabk.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check alabk.out.dif
==============================================================
diffing ./out.save/glybk.out.save with glybk.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check glybk.out.dif
==============================================================
diffing ./out.save/probk.out.save with probk.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check probk.out.dif
==============================================================
diffing ./out.save/da.out.save with da.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check da.out.dif
==============================================================
diffing ./out.save/dc.out.save with dc.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check dc.out.dif
==============================================================
diffing ./out.save/dg.out.save with dg.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check dg.out.dif
==============================================================
diffing ./out.save/dt.out.save with dt.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check dt.out.dif
==============================================================
diffing ./out.save/ru.out.save with ru.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check ru.out.dif
==============================================================
diffing ./out.save/arg.out.save with arg.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check arg.out.dif
==============================================================
diffing ./out.save/asp.out.save with asp.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check asp.out.dif
==============================================================
diffing ./out.save/cym.out.save with cym.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check cym.out.dif
==============================================================
diffing ./out.save/glu.out.save with glu.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check glu.out.dif
==============================================================
diffing ./out.save/hip.out.save with hip.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check hip.out.dif
==============================================================
diffing ./out.save/lys.out.save with lys.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check lys.out.dif
==============================================================
diffing ./out.save/dap.out.save with dap.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check dap.out.dif
==============================================================
diffing ./out.save/da3p.out.save with da3p.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check da3p.out.dif
==============================================================
diffing ./out.save/da5p.out.save with da5p.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check da5p.out.dif
==============================================================
diffing ./out.save/danp.out.save with danp.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check danp.out.dif
==============================================================
diffing ./out.save/rap.out.save with rap.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check rap.out.dif
==============================================================
diffing ./out.save/ra3p.out.save with ra3p.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check ra3p.out.dif
==============================================================
diffing ./out.save/ra5p.out.save with ra5p.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check ra5p.out.dif
==============================================================
diffing ./out.save/ranp.out.save with ranp.out
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check ranp.out.dif
==============================================================
cd pbsa_tsr && ./Run.tsrb.min
diffing mdout.tsrb.min.save with mdout.tsrb.min
PASSED
==============================================================
cd pbsa_decres && ./Run.pbsa_decres
diffing mdout.pbsa_decres.save with mdout.pbsa_decres
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check mdout.pbsa_decres.dif
==============================================================
cd pbsa_decpw && ./Run.pbsa_decpw
diffing mdout.pbsa_decpw.save with mdout.pbsa_decpw
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE: check mdout.pbsa_decpw.dif
==============================================================
cd ambpdb && ./Run.ambpdb
| New format PARM file being parsed.
| Version = 1.000 Date = 02/19/04 Time = 15:33:29
diffing restrt.pdb.save with restrt.pdb
PASSED
==============================================================
cd ambpdb_first_protein && ./Run.ambpdb
| New format PARM file being parsed.
| Version = 1.000 Date = 02/15/07 Time = 16:57:28
diffing first.pdb.save with first.pdb
possible FAILURE: check first.pdb.dif
==============================================================
cd ambpdb_first_rna && ./Run.ambpdb
| New format PARM file being parsed.
| Version = 1.000 Date = 05/18/06 Time = 18:52:52
diffing first.pdb.save with first.pdb
possible FAILURE: check first.pdb.dif
==============================================================
cd elsize && ./Run.elsize
../../exe/elsize: Command not found.
./Run.elsize: Program error
so do I need to change a file or do a static build? I tried static before and it didn't get much further.
Thanks,
Jeff
Jeffrey Sanders, B.S.
PhD Candidate
Program in Structural Biology and
Molecular Pharmacology
233 S. 10th st.
Bluemle Life Science Building 209
Philadelphia, PA 19107
Office: 215-955-1361
Cell: 856-693-3164
Email: jeffrey.sanders.jefferson.edu
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Received on Tue Sep 21 2010 - 09:30:05 PDT
