From: Cezary Czaplewski Date: Mon, 18 Feb 2013 07:46:11 +0000 (+0100) Subject: dynamic dissulfides with finegrain parallelization X-Git-Tag: v.3.2~16 X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=commitdiff_plain;h=62fe06d61bc188d9cda760c882e237aa472e47dc dynamic dissulfides with finegrain parallelization --- diff --git a/bin/unres/MD/unres_gfortran_single_E0LL2Y.exe b/bin/unres/MD/unres_gfortran_single_E0LL2Y.exe index 4e086ce..98d46b9 100755 Binary files a/bin/unres/MD/unres_gfortran_single_E0LL2Y.exe and b/bin/unres/MD/unres_gfortran_single_E0LL2Y.exe differ diff --git a/bin/unres/MD/unres_gfortran_single_GAB.exe b/bin/unres/MD/unres_gfortran_single_GAB.exe index fbdcabb..9259f78 100755 Binary files a/bin/unres/MD/unres_gfortran_single_GAB.exe and b/bin/unres/MD/unres_gfortran_single_GAB.exe differ diff --git a/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe b/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe new file mode 100755 index 0000000..c9769dd Binary files /dev/null and b/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe differ diff --git a/bin/unres/MD/unres_ifort_MPICH_GAB.exe b/bin/unres/MD/unres_ifort_MPICH_GAB.exe new file mode 100755 index 0000000..c8defa0 Binary files /dev/null and b/bin/unres/MD/unres_ifort_MPICH_GAB.exe differ diff --git a/bin/unres/MD/unres_ifort_single_E0LL2Y.exe b/bin/unres/MD/unres_ifort_single_E0LL2Y.exe index 651864e..6b3cf7c 100755 Binary files a/bin/unres/MD/unres_ifort_single_E0LL2Y.exe and b/bin/unres/MD/unres_ifort_single_E0LL2Y.exe differ diff --git a/bin/unres/MD/unres_ifort_single_GAB.exe b/bin/unres/MD/unres_ifort_single_GAB.exe new file mode 100755 index 0000000..93d0028 Binary files /dev/null and b/bin/unres/MD/unres_ifort_single_GAB.exe differ diff --git a/source/unres/src_MD/Makefile_lnx_ifc10_opteron b/source/unres/src_MD/Makefile_lnx_ifc10_opteron deleted file mode 100644 index 13c3249..0000000 --- a/source/unres/src_MD/Makefile_lnx_ifc10_opteron +++ /dev/null @@ -1,143 +0,0 @@ -CPPFLAGS = -DPROCOR -DLINUX -DUNRES -DMP -DMPI -DPGI -DISNAN \ - -DSPLITELE -DAMD64 -DLANG0 -# -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -#-DCRYST_TOR -# -DPROCOR -# -DTSCSC -#-DTIMING \ -# -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -# -DMOMENT -#-DPARVEC -#-DPARINT -DPARINTDER - -INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh - - -FC= ifort - -OPT = -O3 -ip -w - -FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include -FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)/include -FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include -FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report -I$(INSTALL_DIR)/include - - -BIN = ../bin/unres_Tc_procor_new_em64_nh_hremd_92110.exe -LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf_em64/libxdrf.a -lpthread - -ARCH = LINUX -PP = /lib/cpp -P - - -all: unres - -.SUFFIXES: .F -.F.o: - ${FC} ${FFLAGS} ${CPPFLAGS} $*.F - - -object = unres.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.o \ - matmult.o readrtns_CSA.o parmread.o gen_rand_conf.o printmat.o map.o \ - pinorm.o randgens.o rescode.o intcor.o timing.o misc.o intlocal.o \ - cartder.o checkder_p.o econstr_local.o energy_p_new_barrier.o \ - energy_p_new-sep_barrier.o gradient_p.o minimize_p.o sumsld.o \ - cored.o rmdd.o geomout.o readpdb.o regularize.o thread.o fitsq.o mcm.o \ - mc.o bond_move.o refsys.o check_sc_distr.o check_bond.o contact.o djacob.o \ - eigen.o blas.o add.o entmcm.o minim_mcmf.o \ - together.o csa.o minim_jlee.o shift.o diff12.o bank.o newconf.o ran.o \ - indexx.o MP.o compare_s1.o prng_32.o \ - test.o banach.o distfit.o rmsd.o elecont.o dihed_cons.o \ - sc_move.o local_move.o \ - intcartderiv.o lagrangian_lesyng.o\ - stochfric.o kinetic_lesyng.o MD_A-MTS.o moments.o int_to_cart.o \ - surfatom.o sort.o muca_md.o MREMD.o rattle.o gauss.o energy_split-sep.o \ - q_measure.o gnmr1.o - -unres: ${object} - cc -o compinfo compinfo.c - ./compinfo | true - ${FC} ${FFLAGS} cinfo.f - ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN} - - -clean: - /bin/rm *.o *.il - -newconf.o: newconf.f - ${FC} ${FFLAGS} ${CPPFLAGS} newconf.f - -bank.o: bank.F - ${FC} ${FFLAGS} ${CPPFLAGS} bank.F - -diff12.o: diff12.f - ${FC} ${FFLAGS} ${CPPFLAGS} diff12.f - -csa.o: csa.f - ${FC} ${FFLAGS} ${CPPFLAGS} csa.f - -shift.o: shift.F - ${FC} ${FFLAGS} ${CPPFLAGS} shift.F - -ran.o: ran.f - ${FC} ${FFLAGS} ${CPPFLAGS} ran.f - -together.o: together.F - ${FC} ${FFLAGS} ${CPPFLAGS} together.F - -test.o: test.F - ${FC} ${FFLAGS} ${CPPFLAGS} test.F - -chainbuild.o: chainbuild.F - ${FC} ${FFLAGS} ${CPPFLAGS} chainbuild.F - -matmult.o: matmult.f - ${FC} ${FFLAGS} ${CPPFLAGS} matmult.f - -parmread.o : parmread.F - ${FC} ${FFLAGS} ${CPPFLAGS} parmread.F - -intcor.o : intcor.f - ${FC} ${FFLAGS} ${CPPFLAGS} intcor.f - -cartder.o : cartder.F - ${FC} ${FFLAGS} ${CPPFLAGS} cartder.F - -readpdb.o : readpdb.F - ${FC} ${FFLAGS2} ${CPPFLAGS} readpdb.F - -sumsld.o : sumsld.f - ${FC} ${FFLAGS} ${CPPFLAGS} sumsld.f - -cored.o : cored.f - ${FC} ${FFLAGS1} ${CPPFLAGS} cored.f - -rmdd.o : rmdd.f - ${FC} ${FFLAGS} ${CPPFLAGS} rmdd.f - -energy_p_new_barrier.o : energy_p_new_barrier.F - ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new_barrier.F - -gradient_p.o : gradient_p.F - ${FC} ${FFLAGSE} ${CPPFLAGS} gradient_p.F - -energy_p_new-sep_barrier.o : energy_p_new-sep_barrier.F - ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new-sep_barrier.F - -lagrangian_lesyng.o : lagrangian_lesyng.F - ${FC} ${FFLAGSE} ${CPPFLAGS} lagrangian_lesyng.F - -MD_A-MTS.o : MD_A-MTS.F - ${FC} ${FFLAGSE} ${CPPFLAGS} MD_A-MTS.F - -blas.o : blas.f - ${FC} ${FFLAGS1} blas.f - -add.o : add.f - ${FC} ${FFLAGS1} add.f - -eigen.o : eigen.f - ${FC} ${FFLAGS2} eigen.f - -proc_proc.o: proc_proc.c - ${CC} ${CFLAGS} proc_proc.c diff --git a/source/unres/src_MD/Makefile_lnx_ifc10_opteron_oldparm b/source/unres/src_MD/Makefile_lnx_ifc10_opteron_oldparm deleted file mode 100644 index d155fa2..0000000 --- a/source/unres/src_MD/Makefile_lnx_ifc10_opteron_oldparm +++ /dev/null @@ -1,143 +0,0 @@ -CPPFLAGS = -DPROCOR -DLINUX -DUNRES -DMP -DMPI -DPGI -DISNAN \ - -DSPLITELE -DAMD64 -DLANG0 \ - -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -#-DCRYST_TOR -# -DPROCOR -# -DTSCSC -#-DTIMING \ -# -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -# -DMOMENT -#-DPARVEC -#-DPARINT -DPARINTDER - -INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh - - -FC= ifort - -OPT = -O3 -ip -w - -FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include -FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)/include -FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include -FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report -I$(INSTALL_DIR)/include - - -BIN = ../bin/unres_Tc_procor_old_em64_nh_hremd_92110.exe -LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf_em64/libxdrf.a -lpthread - -ARCH = LINUX -PP = /lib/cpp -P - - -all: unres - -.SUFFIXES: .F -.F.o: - ${FC} ${FFLAGS} ${CPPFLAGS} $*.F - - -object = unres.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.o \ - matmult.o readrtns_CSA.o parmread.o gen_rand_conf.o printmat.o map.o \ - pinorm.o randgens.o rescode.o intcor.o timing.o misc.o intlocal.o \ - cartder.o checkder_p.o econstr_local.o energy_p_new_barrier.o \ - energy_p_new-sep_barrier.o gradient_p.o minimize_p.o sumsld.o \ - cored.o rmdd.o geomout.o readpdb.o regularize.o thread.o fitsq.o mcm.o \ - mc.o bond_move.o refsys.o check_sc_distr.o check_bond.o contact.o djacob.o \ - eigen.o blas.o add.o entmcm.o minim_mcmf.o \ - together.o csa.o minim_jlee.o shift.o diff12.o bank.o newconf.o ran.o \ - indexx.o MP.o compare_s1.o prng_32.o \ - test.o banach.o distfit.o rmsd.o elecont.o dihed_cons.o \ - sc_move.o local_move.o \ - intcartderiv.o lagrangian_lesyng.o\ - stochfric.o kinetic_lesyng.o MD_A-MTS.o moments.o int_to_cart.o \ - surfatom.o sort.o muca_md.o MREMD.o rattle.o gauss.o energy_split-sep.o \ - q_measure.o gnmr1.o - -unres: ${object} - cc -o compinfo compinfo.c - ./compinfo | true - ${FC} ${FFLAGS} cinfo.f - ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN} - - -clean: - /bin/rm *.o *.il - -newconf.o: newconf.f - ${FC} ${FFLAGS} ${CPPFLAGS} newconf.f - -bank.o: bank.F - ${FC} ${FFLAGS} ${CPPFLAGS} bank.F - -diff12.o: diff12.f - ${FC} ${FFLAGS} ${CPPFLAGS} diff12.f - -csa.o: csa.f - ${FC} ${FFLAGS} ${CPPFLAGS} csa.f - -shift.o: shift.F - ${FC} ${FFLAGS} ${CPPFLAGS} shift.F - -ran.o: ran.f - ${FC} ${FFLAGS} ${CPPFLAGS} ran.f - -together.o: together.F - ${FC} ${FFLAGS} ${CPPFLAGS} together.F - -test.o: test.F - ${FC} ${FFLAGS} ${CPPFLAGS} test.F - -chainbuild.o: chainbuild.F - ${FC} ${FFLAGS} ${CPPFLAGS} chainbuild.F - -matmult.o: matmult.f - ${FC} ${FFLAGS} ${CPPFLAGS} matmult.f - -parmread.o : parmread.F - ${FC} ${FFLAGS} ${CPPFLAGS} parmread.F - -intcor.o : intcor.f - ${FC} ${FFLAGS} ${CPPFLAGS} intcor.f - -cartder.o : cartder.F - ${FC} ${FFLAGS} ${CPPFLAGS} cartder.F - -readpdb.o : readpdb.F - ${FC} ${FFLAGS2} ${CPPFLAGS} readpdb.F - -sumsld.o : sumsld.f - ${FC} ${FFLAGS} ${CPPFLAGS} sumsld.f - -cored.o : cored.f - ${FC} ${FFLAGS1} ${CPPFLAGS} cored.f - -rmdd.o : rmdd.f - ${FC} ${FFLAGS} ${CPPFLAGS} rmdd.f - -energy_p_new_barrier.o : energy_p_new_barrier.F - ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new_barrier.F - -gradient_p.o : gradient_p.F - ${FC} ${FFLAGSE} ${CPPFLAGS} gradient_p.F - -energy_p_new-sep_barrier.o : energy_p_new-sep_barrier.F - ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new-sep_barrier.F - -lagrangian_lesyng.o : lagrangian_lesyng.F - ${FC} ${FFLAGSE} ${CPPFLAGS} lagrangian_lesyng.F - -MD_A-MTS.o : MD_A-MTS.F - ${FC} ${FFLAGSE} ${CPPFLAGS} MD_A-MTS.F - -blas.o : blas.f - ${FC} ${FFLAGS1} blas.f - -add.o : add.f - ${FC} ${FFLAGS1} add.f - -eigen.o : eigen.f - ${FC} ${FFLAGS2} eigen.f - -proc_proc.o: proc_proc.c - ${CC} ${CFLAGS} proc_proc.c diff --git a/source/unres/src_MD/Makefile_single_ifort b/source/unres/src_MD/Makefile_single_ifort index 245206b..c651e39 100644 --- a/source/unres/src_MD/Makefile_single_ifort +++ b/source/unres/src_MD/Makefile_single_ifort @@ -43,7 +43,7 @@ object = unres.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.o \ intcartderiv.o lagrangian_lesyng.o\ stochfric.o kinetic_lesyng.o MD_A-MTS.o moments.o int_to_cart.o \ surfatom.o sort.o muca_md.o MREMD.o rattle.o gauss.o energy_split-sep.o \ - q_measure.o gnmr1.o test.o + q_measure.o gnmr1.o test.o ssMD.o GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES -DISNAN \ -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC diff --git a/source/unres/src_MD/cinfo.f b/source/unres/src_MD/cinfo.f index 26b5cab..5d23d6b 100644 --- a/source/unres/src_MD/cinfo.f +++ b/source/unres/src_MD/cinfo.f @@ -1,10 +1,10 @@ C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C -C 3 1 79 +C 3 1 92 subroutine cinfo include 'COMMON.IOUNITS' write(iout,*)'++++ Compile info ++++' - write(iout,*)'Version 3.1 build 79' - write(iout,*)'compiled Sun Feb 17 14:00:16 2013' + write(iout,*)'Version 3.1 build 92' + write(iout,*)'compiled Mon Feb 18 04:11:12 2013' write(iout,*)'compiled by czarek@piasek3' write(iout,*)'OS name: Linux ' write(iout,*)'OS release: 2.6.32-42-generic ' diff --git a/source/unres/src_MD/energy_p_new_barrier.F b/source/unres/src_MD/energy_p_new_barrier.F index 8a9a3eb..2557051 100644 --- a/source/unres/src_MD/energy_p_new_barrier.F +++ b/source/unres/src_MD/energy_p_new_barrier.F @@ -1589,6 +1589,8 @@ C IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN call dyn_ssbond_ene(i,j,evdwij) evdw=evdw+evdwij + if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') + & 'evdw',i,j,evdwij,' ss' ELSE ind=ind+1 itypj=itype(j) diff --git a/source/unres/src_MD/parmread.F b/source/unres/src_MD/parmread.F index 62a0ddf..030d64e 100644 --- a/source/unres/src_MD/parmread.F +++ b/source/unres/src_MD/parmread.F @@ -565,7 +565,8 @@ cc maxinter is maximum interaction sites do l=1,maxinter do i=1,nsccortyp do j=1,nsccortyp - read (isccor,*,end=1113,err=1113) nterm_sccor(i,j),nlor_sccor(i,j) + read (isccor,*,end=1113,err=1113) nterm_sccor(i,j), + & nlor_sccor(i,j) v0ijsccor=0.0d0 si=-1.0d0 diff --git a/source/unres/src_MD/readrtns.F b/source/unres/src_MD/readrtns.F index 10cde78..332a2f7 100644 --- a/source/unres/src_MD/readrtns.F +++ b/source/unres/src_MD/readrtns.F @@ -1251,18 +1251,6 @@ C Generate distance constraints, if the PDB structure is to be regularized. write (iout,'(20i4)') (iss(i),i=1,ns) if (dyn_ss) then write(iout,*)"Running with dynamic disulfide-bond formation" - do i=nss+1,nhpb - ihpb(i-nss)=ihpb(i) - jhpb(i-nss)=jhpb(i) - forcon(i-nss)=forcon(i) - dhpb(i-nss)=dhpb(i) - enddo - nhpb=nhpb-nss - nss=0 - call hpb_partition - do i=1,ns - dyn_ss_mask(iss(i))=.true. - enddo else write (iout,'(/a/)') 'Pre-formed links are:' do i=1,nss @@ -1270,14 +1258,27 @@ C Generate distance constraints, if the PDB structure is to be regularized. i2=jhpb(i)-nres it1=itype(i1) it2=itype(i2) - if (me.eq.king.or..not.out1file) - & write (iout,'(2a,i3,3a,i3,a,3f10.3)') + write (iout,'(2a,i3,3a,i3,a,3f10.3)') & restyp(it1),'(',i1,') -- ',restyp(it2),'(',i2,')',dhpb(i), & ebr,forcon(i) enddo write (iout,'(a)') endif endif + if (ns.gt.0.and.dyn_ss) then + do i=nss+1,nhpb + ihpb(i-nss)=ihpb(i) + jhpb(i-nss)=jhpb(i) + forcon(i-nss)=forcon(i) + dhpb(i-nss)=dhpb(i) + enddo + nhpb=nhpb-nss + nss=0 + call hpb_partition + do i=1,ns + dyn_ss_mask(iss(i))=.true. + enddo + endif if (i2ndstr.gt.0) call secstrp2dihc c call geom_to_var(nvar,x) c call etotal(energia(0))