[AMBER] building premed for Intel Xeon Phi coprocessors (offload mode)

From: Song-Ho Chong <chong.sookmyung.ac.kr>
Date: Wed, 15 Feb 2017 16:04:21 +0900

Dear Amber Developers,

We got an opportunity to use a test server which is equipped with
Intel Xeon Phi 7210 (64 cores) and where the latest Intel Parallel
Studio XE is installed.

Following the Amber manual, we proceeded as

2) ./configure -mic_offload intel
3) make install

However, at the end, we got the following error message:

mpiifort -ip -O3 -no-prec-div -xHost -DMIC_offload -qopenmp
-qopt-streaming-cache-evict=0 -fimf-domain-exclusion=15 -align array64byte
-o /opt/apps/amber16/bin/pmemd.mic_offload.MPI gbl_constants.o
gbl_datatypes.o state_info.o file_io_dat.o mdin_ctrl_dat.o mdin_emil_dat.o
mdin_ewald_dat.o mdin_debugf_dat.o prmtop_dat.o inpcrd_dat.o dynamics_dat.o
emil.o img.o nbips.o offload_allocation.o parallel_dat.o parallel.o
gb_parallel.o pme_direct.o pme_recip_dat.o pme_slab_recip.o pme_blk_recip.o
pme_slab_fft.o pme_blk_fft.o pme_fft_dat.o fft1d.o bspline.o pme_force.o
pbc.o nb_pairlist.o gb_ene_hybrid.o nb_exclusions.o cit.o dynamics.o
bonds.o angles.o dihedrals.o extra_pnts_nb14.o runmd.o loadbal.o shake.o
prfs.o mol_list.o runmin.o constraints.o axis_optimize.o gb_ene.o veclib.o
gb_force.o timers.o pmemd_lib.o runfiles.o file_io.o AmberNetcdf.o
bintraj.o binrestart.o pmemd_clib.o pmemd.o random.o degcnt.o erfcfun.o
nmr_calls.o nmr_lib.o get_cmdline.o master_setup.o pme_alltasks_setup.o
pme_setup.o ene_frc_splines.o gb_alltasks_setup.o nextprmtop_section.o
angles_ub.o dihedrals_imp.o cmap.o charmm.o charmm_gold.o findmask.o remd.o
multipmemd.o remd_exchg.o amd.o gamd.o ti.o gbsa.o barostats.o scaledMD.o
constantph.o energy_records.o constantph_dat.o relaxmd.o sgld.o emap.o
get_efield_energy.o -L/opt/apps/amber16/lib
/opt/apps/amber16/lib/libnetcdff.a /opt/apps/amber16/lib/libnetcdf.a
-shared-intel /opt/apps/amber16/lib/libemil.a -lstdc++

ifort: warning #10362: Environment configuration problem encountered.
Please check for proper MPSS installation and environment setup.

x86_64-k1om-linux-ld: No such file or directory

make[3]: *** [/opt/apps/amber16/bin/pmemd.mic_offload.MPI] Error 100

make[3]: Leaving directory `/opt/apps/amber16/src/pmemd/src'

make[2]: *** [mic_offload] Error 2

make[2]: Leaving directory `/opt/apps/amber16/src/pmemd'

make[1]: *** [mic_offload] Error 2

make[1]: Leaving directory `/opt/apps/amber16/src'

make: *** [install] Error 2

I just wonder whether this is because 7210 is not officially supported yet,
or because we have some problem in our environment setup.

I would appreciate it very much if you could suggest any idea on this.

Best wishes,
Song-Ho Chong
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Received on Tue Feb 14 2017 - 23:30:02 PST
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