Package Details: vmd-src 1.9.4a57-3

Git Clone URL: (read-only, click to copy)
Package Base: vmd-src
Description: Visual Molecular Dynamics
Upstream URL:
Licenses: custom
Conflicts: vmd, vmd-bin
Provides: vmd
Submitter: a.kudelin
Maintainer: a.kudelin
Last Packager: a.kudelin
Votes: 2
Popularity: 0.000000
First Submitted: 2019-05-24 13:23 (UTC)
Last Updated: 2023-06-01 08:51 (UTC)

Dependencies (14)

Required by (3)

Sources (2)

Latest Comments

Kiri0 commented on 2024-02-16 06:06 (UTC) (edited on 2024-02-16 06:06 (UTC) by Kiri0)

Some err happens:

Linking vmd_LINUXAMD64 ...

/usr/bin/ld: cannot find -lmpi_cxx: No such file or directory

collect2: error: ld returned 1 exit status

make: *** [Makefile:688: vmd_LINUXAMD64] Error 1

a.kudelin commented on 2023-06-01 08:52 (UTC)

@koroki, thanks, it's done.

koroki commented on 2023-05-31 09:02 (UTC)

The configure patch must be updated with 3.11 python path.

David01 commented on 2022-11-15 12:15 (UTC) (edited on 2022-11-15 12:16 (UTC) by David01)

@a.kudelin version 1.9.4a57: I have experienced the following problem when displaying Coloring Method=Secondary Structures and Drawing Method=NewCartoon or NewRibbons:

Minimal Working Example:

Download pdb from here:

Otherwise, you can also find it here:

Create representation > Coloring Method=Secondary Structures ; Drawing Method=NewCartoon (also happens with NewRibbons)

You'll see this:

Ondrian commented on 2022-05-04 20:36 (UTC)

The package does not build without mpi (openmpi) which should be added as dependency

VMDMPI.C:18:10: fatal error: mpi.h: No such file or directory
   18 | #include <mpi.h>

wftao commented on 2021-04-02 03:23 (UTC)

It seems that vmd is not compatible with ospray 2.5, I got a lot of compilation errors after ospray upgrade.

a.kudelin commented on 2020-09-20 07:13 (UTC)

@mehedeetalha, you should download the source first from the website.

mehedeetalha commented on 2020-09-19 04:07 (UTC)

Building vmd-src... ==> Making package: vmd-src 1.9.4a43-2 (Sat 19 Sep 2020 10:03:48 AM +06) ==> Checking runtime dependencies... ==> Checking buildtime dependencies... ==> Retrieving sources... ==> ERROR: vmd-1.9.4a43.src.tar.gz was not found in the build directory and is not a URL. Failed to build vmd-src

Ondrian commented on 2020-08-11 12:47 (UTC)

I get an error

Building all supported targets...
Unrecognized host system, add your own switch statement to customize
for your build environment.  Edit build.csh and change the variables
in the section marked XXXNEWPLATFORM.
Populating distribution directory with compiled plugins
mkdir: cannot create directory ‘/include’: Permission denied
cp: cannot create regular file '/include': Permission denied

which can be solved by removing world from line 55 in PKGBUILD.

Afterwards I get error concerning the cuda compute capability.

nvcc -lineinfo --ptxas-options=-v -gencode arch=compute_30,code=compute_30 -gencode arch=compute_30,code=sm_35 -gencode arch=compute_30,code=sm_37 -gencode arch=compute_50,code=compute_50 -gencode arch=compute_50,code=sm_50 -gencode arch=compute_60,code=compute_60 -gencode arch=compute_60,code=sm_60 -gencode arch=compute_70,code=compute_70 -gencode arch=compute_70,code=sm_70 --ftz=true  --machine 64 -O3  -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDOPENGLPBUFFER -DVMDEGLPBUFFER  -DVMDOPENGL -DVMDFLTKOPENGL  -DVMDCOLVARS -DVMDCUDA -DMSMPOT_CUDA -DVMDOPENCL -DVMDMPI  -DVMDIMD -DVMDXINERAMA -DVMDXINPUT -DVMDLIBOSPRAY -DVMDOSPRAY_INTERACTIVE_OPENGL -DVMDLIBPNG -DVMDPYTHON -DVMDTHREADS -DWKFTHREADS -DUSEPOSIXTHREADS -D_REENTRANT -DVMDZLIB -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDLATTICECUBES -DVMDTCL -DVMDTK  -DVMDSTATICPLUGINS  -DVMDGUI -DVMDFLTK  -I/usr/include/CL -I/usr/include    -I/usr/local/ospray-1.8.5.x86_64.linux/include -I/usr/local/ospray-1.8.5.x86_64.linux/ospray/include  -I/Projects/vmd/vmd/lib/libpng/include -I/usr/include/python2.7 -I -I  -I/Projects/vmd/vmd/lib/zlib/include -I../lib/tcl/include -I../lib/tk/include -I../plugins/include -I../plugins/LINUXAMD64/molfile -I../lib/netcdf/include -I../lib/fltk/include -I. -c -o ../LINUXAMD64/msmpot_cuda.o
Compiling  fitrms.c  -->  fitrms.o  ...
Compiling  -->  msmpot_cuda.o  ...
nvcc fatal   : Unsupported gpu architecture 'compute_30'
make: *** [Makefile:621: msmpot_cuda.o] Error 1

I assume this is because the current cuda 11 supports only compute capability 5.2 - 8.0.

This could probably be fixed in configure.patch, but I didn't figure out how.