AMBER Archive (2004)

Subject: Re: AMBER: Amber8 compilation error

From: Arvind (
Date: Fri Apr 30 2004 - 14:50:38 CDT

On Fri, 30 Apr 2004, David A. Case wrote:

> We have not seen this in either small memory or large memory alitx systems.
> Use the "limits" command to check your shell limits, and increase anything
> that looks small. Are other (big memory) jobs running on your altix when
> this compilation is attempted?
> (I'm assuming that "make serial" worked that correct?)
> ...regards...dac

Dear Dr. DAC,
i was trying to gauge how parallel compilation works, so
i had only tried 'make parallel'. Just now, i tried

        ./configure -nopar

        make serial

But again the compilation runs into an (apparently similar) error after a
while. Here is the tail of the message:

make[3]: warning: Clock skew detected. Your build may be incomplete.
make[3]: Leaving directory `/global/utemp/mbumravi/amber8/src/lmod/lmod'
ar rv lmod.a xmin/*.o nvib/*.o lmod/*.o
a - xmin/xmin.o
a - nvib/nvib.o
a - lmod/lmod.o
ranlib lmod.a
make[2]: warning: Clock skew detected. Your build may be incomplete.
make[2]: Leaving directory `/global/utemp/mbumravi/amber8/src/lmod'
ifort -FR -o sander trace.o lmod.o decomp.o icosasurf.o egb.o findmask.o
pb_fo rce.o
sander.o cshf.o noecalc.o noeread.o caldis.o calrate.o dinten.o drates.o i
ndexn.o kmat.o pearsn.o plane.o remarc.o nmrcal.o nmrred.o restal.o
getnat.o nmr
nrg.o modwt.o disnrg.o angnrg.o tornrg.o nmrprt.o nmrgrp.o nmrcms.o
nmrcmf.o imp
num.o nmrsht.o at2res.o chklin.o opnmrg.o printe.o runmin.o ndvprt.o
force.o rdp
arm.o mdread.o locmem.o runmd.o getcor.o r6ave.o r6drv.o aveint.o degcnt.o
corf. o
threeb.o tripl.o nmrrad.o decnvh.o fastwt.o echoin.o parallel.o jnrg.o
shake.o ene.o
mdwrit.o minrit.o set.o setmm.o dynlib.o mdfil.o nmlsrc.o ew_force.o ew_s
etup.o ew_box.o ew_bspline.o ew_fft.o ew_direct.o ew_recip.o pcshift.o
align.o r
stack.o istack.o rfree.o rgroup.o random.o lsqfit.o amopen.o debug.o
ew_recip_re g.o
ew_handle_dips.o ew_dipole_recip.o mexit.o new_time.o extra_pts.o
thermo_int .o
matinv.o assert.o mmtsb.o mmtsb_client.o erfcfun.o veclib.o mdm.o
pb_init.o c
onstantph.o prn_dipoles.o \
        ../lmod/lmod.a -lscs \
        ../lapack/lapack.a ../blas/blas.a ../lib/nxtsec.o ../lib/sys.a
../lib/sys.a: could not read symbols: Memory exhausted
make[1]: *** [sander] Error 1
make[1]: Leaving directory `/global/utemp/mbumravi/amber8/src/sander'
make: *** [serial] Error 2

I don't think this is a system memory problem because i've tried this at
different times and always it stumbles at the same point. Again right now,
i can see that there are no highend (big memory) jobs running and there
is a lot of free memory, but still i get the same problem.

Does someone out there have an idea what's going on? Thanx in advance.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to