Re: AMBER: error with compiling amber8 with lam on intel pc clusters

From: Xuebin Qiao <xbqiao.gmail.com>
Date: Thu, 15 Dec 2005 15:57:24 +0800

Hi,

Maybe you have used pgi to compile lam7 source.

best regards

On 12/15/05, Ye Mei <ymei.itcc.nju.edu.cn> wrote:
>
> Dear Amber usersúČ
>
> when I tried to compile amber8 with lam and ifort on my intel pc cluster,
> it failed with error message:
> ifort -FR -o sander trace.o lmod.o decomp.o icosasurf.o egb.o
> findmask.o pb_force.o sander.o cshf.o noecalc.o noeread.o caldis.o
> calrate.o dinten.o drates.o indexn.o kmat.o pearsn.o plane.o remarc.o
> nmrcal.o nmrred.o restal.o getnat.o nmrnrg.o modwt.o disnrg.o angnrg.o
> tornrg.o nmrprt.o nmrgrp.o nmrcms.o nmrcmf.o impnum.o nmrsht.o at2res.o
> chklin.o opnmrg.o printe.o runmin.o ndvprt.o force.o rdparm.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.oew_force.o ew_setup.o ew_box.o ew_bspline.o ew_fft.o ew_direct.o ew_recip.o
> pcshift.o align.o rstack.o istack.o rfree.o rgroup.o random.o lsqfit.o
> amopen.o debug.o ew_recip_reg.o ew_handle_dips.o ew_dipole_recip.o mexit.onew_time.o extra_pts.o thermo_int.o
> matinv.o assert.o mmtsb.o mmtsb_client.o erfcfun.o veclib.o mdm.opb_init.o
> constantph.o prn_dipoles.o \
> ../lmod/lmod.a -L/usr/local/lam/lib -llammpio -llamf77mpi -lmpi
> -llam -lutil -lpthread -lsvml -L/usr/intel/imkl/mkl80/lib/32 -lvml
> -lmkl_lapack64 -lmkl -lguide -lpthread \
> ../lapack/lapack.a ../blas/blas.a ../lib/nxtsec.o ../lib/sys.a
> /usr/local/lam/lib/libmpi.a(lamonesided.o)(.text+0x876): In function
> `lam_accumulate':
> : undefined reference to `__mth_i_kmul'
> /usr/local/lam/lib/libmpi.a(lamonesided.o)(.text+0x972): In function
> `lam_accumulate':
> : undefined reference to `__mth_i_kmul'
> /usr/local/lam/lib/libmpi.a(lamonesided.o)(.text+0xaea): In function
> `lam_put':
> : undefined reference to `__mth_i_kmul'
> /usr/local/lam/lib/libmpi.a(lamonesided.o)(.text+0xb7a): In function
> `lam_get':
> : undefined reference to `__mth_i_kmul'
> /usr/local/lam/lib/libmpi.a(lamreduce.o)(.text+0x341): In function
> `lam_max':
> : undefined reference to `__mth_i_kcmp'
> /usr/local/lam/lib/libmpi.a(lamreduce.o)(.text+0x3b5): In function
> `lam_max':
> : undefined reference to `__mth_i_kucmp'
> /usr/local/lam/lib/libmpi.a(lamreduce.o)(.text+0x761): In function
> `lam_min':
> : undefined reference to `__mth_i_kcmp'
> /usr/local/lam/lib/libmpi.a(lamreduce.o)(.text+0x7d5): In function
> `lam_min':
> : undefined reference to `__mth_i_kucmp'
> /usr/local/lam/lib/libmpi.a(lamreduce.o)(.text+0x1169): In function
> `lam_prod':
> : undefined reference to `__mth_i_kmul'
> /usr/local/lam/lib/libmpi.a(lamreduce.o)(.text+0x11dc): In function
> `lam_prod':
> : undefined reference to `__mth_i_kmul'
> /usr/local/lam/lib/libmpi.a(types.o)(.data+0x2c): In function
> `lam_tv_load_type_defs':
> /root/lam-7.0.4/share/mpi/totalview/types.c:55: undefined reference to
> `__pgdbg_stub'
> make[1]: *** [sander] Error 1
> make[1]: Leaving directory `/home/ymei/amber8/src/sander'
> make: *** [parallel] Error 2
>
> It seems that it need some library of pgi compiler. So I tried pgi
> compiler, and the compilation completed successfully.
> I feel puzzled with this message, especially the last line.
> /root/lam-7.0.4/share/mpi/totalview/types.c:55: undefined reference to
> `__pgdbg_stub'
>
> Who can help me out of it?
>
>
> Best regards,
>
> Ye Mei
> ymei.itcc.nju.edu.cn
> Institute of Theoretical and Computational Chemistry
> Key Laboratory of Mesoscopic Chemistry
> School of Chemistry and Chemical Engineering
> Nanjing University
> Nanjing 210093
> P.R.China
> 2005-12-15
>
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--
... there have been two really clean,
consistent models of programming so far:
the C model and the Lisp model.
These two seem points of high ground,
with swampy lowlands between them.
                                      --Paul Graham
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Received on Thu Dec 15 2005 - 08:53:00 PST
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