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View Code? Open in Web Editor NEWInstructions for how to package VMD for Ubuntu and not pull your hair out in the process.
License: Creative Commons Zero v1.0 Universal
Instructions for how to package VMD for Ubuntu and not pull your hair out in the process.
License: Creative Commons Zero v1.0 Universal
root@3f57aa8c8953:/vmdpackaging/vmd-1.9.4a57# debuild -b
dpkg-buildpackage -us -uc -ui -b
dpkg-buildpackage: info: source package vmd
dpkg-buildpackage: info: source version 1.9.4a55-3
dpkg-buildpackage: info: source distribution focal
dpkg-buildpackage: info: source changed by Josh Vermaas <[email protected]>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
dpkg-checkbuilddeps: error: Unmet build dependencies: python3.8-dev
dpkg-buildpackage: warning: build dependencies/conflicts unsatisfied; aborting
dpkg-buildpackage: warning: (Use -d flag to override.)
debuild: fatal error at line 1182:
dpkg-buildpackage -us -uc -ui -b failed
root@3f57aa8c8953:/vmdpackaging/vmd-1.9.4a57# debuild -d
This package has a Debian revision number but there does not seem to be
an appropriate original tar file or .orig directory in the parent directory;
(expected one of vmd_1.9.4a55.orig.tar.gz, vmd_1.9.4a55.orig.tar.bz2,
vmd_1.9.4a55.orig.tar.lzma, vmd_1.9.4a55.orig.tar.xz or vmd-1.9.4a57.orig)
continue anyway? (y/n) y
this ends up working.
The three issues I came across are
cd .. #Puts you in the right directory.
sudo dpkg -i vmd-cuda_1.9.4a57-1_amd64.deb vmd-plugins_1.9.4a55-1_amd64.deb
to
cd .. #Puts you in the right directory.
sudo dpkg -i vmd-cuda_1.9.4a55-3_amd64.deb vmd-plugins_1.9.4a55-3_amd64.deb
Hello,
Thanks for making these instructions available!! Everything works perfectly until I try to get support for either OSPRay or OptiX.
When I try to build with OSPRay by uncommenting this line in the Makefile, I get debuild_lospcommon.txt (/usr/bin/ld: cannot find -lospcommon: No such file or directory
)
If I replace -lospcommon
with -lrkcommon
in edited/configure, I get:
debuild_rkcommon.txt. Then, launching VMD gives me:
Info) VMD for LINUXAMD64, version 1.9.4a57 (August 11, 2023)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to [email protected]
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 16 CPUs.
Info) CPU features: SSE2 SSE4.1 AVX AVX2 FMA F16 AVX512F AVX512CD HT
Info) Free system memory: 12GB (75%)
Info) Creating CUDA device pool and initializing hardware...
Info) Detected 1 available CUDA accelerator::
Info) [0] NVIDIA GeForce RTX 3070 Laptop GPU 40 SM_8.6 1.6 GHz, 7.8GB RAM SP32 KT AE2 ZC
Info) OpenGL renderer: Mesa Intel(R) UHD
Graphics (TGL GT1)
Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFS)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (16384x16384), 3-D (512x512x512), Multitexture (8)
OSPRay2Renderer) OSPRay_Global_Init
Segmentation fault (core dumped)
If I uncomment the OptiX line in the Makefile (and re-comment the OSPRay line), I get debuild_optix.txt. I don't know how to parse this output, so it's not clear to me what is going wrong.
I know that ospcommon exists, but I get an error Threading Building Blocks (TBB) with minimum version 4.4 not found.
that I'm not sure whether I should dig into? I do have libtbb-dev
installed.
Dear prof Vermaas, I hope that you are fine.
I want ask you, How do I install vmd with FastPBC? . I have review your README here, but it mention any lines from code that I am not sure if are the corrects.
tcl_commands.C I found the following section containing fastpbc name, Do I change from 0 to 1?
#if 0
Tcl_CreateObjCommand(interp, "fastpbc", obj_fastpbc,
(ClientData) app, (Tcl_CmdDeleteProc *) NULL);
#endif
now in same file in line 283 I found ,
282 Tcl_CreateCommand(interp, "vmd_menu", text_cmd_menu,
283 (ClientData) app, (Tcl_CmdDeleteProc *) NULL);
In this file (tcl_commands.C) I don't found more code that refer to FastPBC
For other hand, I want to ask you, Is this fastPBC suitable to box with cubic and rectangular geometries?
I need any very fast tool that PBCTools (the tcl program in VMD), because I have a 25K frames with 600K atoms, and a lot of replicas (>18) , and I only have workstation to perform this calculations. I have try using qwrap, too, but this less flexible.
Thanks so much in advanced for your help.
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