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vmd-packaging-instructions's Issues

Errors with "debuild -b" command

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

  1. python dependency problem, wants 3.8 but you install 3.10
  2. revision number (perhaps this file needs to be updated changelog)
  3. install command needs small change
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

Error installing with OSPRay or OptiX

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.

vmd with FastPBC

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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