![install vmd install vmd](https://www.intel.com/content/dam/support/us/en/images/memory-and-storage/57787_image1.png)
The next stage is to build the plugins for VMD. Tail -f Make.out # Ctrl-C to stop followingĪs prep, create the directory where plugins will be installed:Įxport PLUGINDIR=$VMDHOME/lib/vmd/plugins Makefile - comment out line 17, and add a line after it:ĬFLAGS=-O3 -static -no-prec-div -xSSE2 -ipo Once complete, copy several tachyon files to the appropriate placesĬd $VMDSRCDIR/vmd-1.9.1/lib/tachyon/compile/linux-64-thr-iccĬp tachyon $VMDSRCDIR/vmd-1.9.1/lib/tachyon/tachyon_LINUXAMD64Ĭp libtachyon.a $VMDSRCDIR/vmd-1.9.1/lib/tachyon/lib_LINUXAMD64ĪCTC is a triangle mesh consolidator. Tail -f Make.out # Ctrl-C to stop following output "CFLAGS = -O3 -static -no-prec-div -xSSE2 -ipo -pthread -fomit-frame-pointer -DLinux -DLP64 -DTHR -D_REENTRANT $(MISCFLAGS)" \ VMD requires version 0.99 or higherĬreate a new "arch" type by adding the following to the file Make-arch - note that this is a Makefile, so the initial whitespace on the line "$(MAKE) all" is a single TAB character: Once this is done, the executable surf is produced. Tail -f Make.out # Ctrl-C to stop following the file LINCLUDE = -L$(MKLROOT)/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lmĬFLAGS = -O3 -static -no-prec-div -ipo -xSSE2 -pthread $(FLAGS) $(INCLUDE)Īnd insert a statement before line 59 so that lines 58-60 are: Make a copy of it:Īnd edit so that the first 9 lines are deleted and replaced with the following 5 lines: There will be many warnings which can be ignored.
#INSTALL VMD ARCHIVE#
The source is provided in the vmd-1.9.1.tar.gz archive
#INSTALL VMD CODE#
Since the original authors of SURF no longer make the source code available. Tail -f Make.out # Ctrl-C to stop following the output P_model.c p_compnd.c report.c nsc.c area.c ssbond.c chk_res.c \Ĭhk_atom.c turn.c pdbasn.c dssp.c outseq.c chkchain.c elem.c measure.c \ P_rem.c p_atom.c p_helix.c p_sheet.c p_turn.c p_ssbond.c p_expdta.c \ Molscr.c die.c hydrbond.c mergepat.c fillasn.c escape.c p_jrnl.c \ Hbenergy.c memory.c helix.c sheet.c rdmap.c phipsi.c command.c \ Thr2one.c one2thr.c filename.c tolostr.c strutil.c place_h.c \ SOURCE = stride.c splitstr.c rdpdb.c initchn.c geometry.c \ LDFLAGS = -L$(MKLROOT)/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm CC = icc -O3 -static -ipo -xSSE2 -no-prec-div -pthread -I$(MKLROOT)/include Makefiles are sensitive to whitespace - there is a difference between TAB and SPACE. IMPORTANT you cannot just copy and paste this. We use the version of STRIDE archived by the VMD team.Įdit the file stride.h, and change line 43 to:Īlso, edit stride.c, and change line 96 from "return(SUCCESS) " to:Ĭreate your own makefile named ac. VMD depends on several external programs, some of which have to be compiled. In general, we will redirect all make output to a file so that any error messages will be captured and not scroll off the screen. This creates two directories: vmd-1.9.1 and plugins.
![install vmd install vmd](https://cdn-ak.f.st-hatena.com/images/fotolife/w/wand_ta/20190312/20190312213131.png)
Set up your environment to use the Intel compilers:Įxport VMDHOME ~/Applications/vmd-1.9.1 # tcsh: setenv VMDHOME ~/Applications/vmd-1.9.1Ĭreate a directory to contain all the VMD-related source code:Įxport VMDSRCDIR=~/src/vmd # this is for bash for tcsh/csh, do "setenv VMDSRCDIR ~src/vmd"ĭownload and expand the source code in that directory: Here is a non-exhaustive list of prerequisite packages (as provided by RedHat):įirst, read the official compilation guide. Neither is required but will greatly speed up execution.
#INSTALL VMD SOFTWARE#
If an NVIDIA graphics card is installed, and if the CUDA GPU programming software development kit is installed, it can take advantage of both. It requires 3D graphics libraries (OpenGL, MESA) to function. The source code is available at the VMD website.
![install vmd install vmd](https://lammpstube.com/wp-content/uploads/2020/03/f5-1200x671.png)
Currently installed on the cluster is version 1.9.1.