VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jan 07 2021 - 17:29:43 CST

On Thu, Jan 7, 2021 at 6:25 PM Chris Taylor <christay_at_usc.edu> wrote:

> Here’s what I did- I’m following the installation instructions in the
> programmer’s manual, but I don’t think I missed anything (maybe I did).
>
>
>
> I cd’d into the source directory and added this to the configure.options:
>
>
>
> [ec2-user_at_ip-172 vmd-1.9.4a51]$ cat configure.options
>
> LINUX MESA FLTK TK ACTC MPI LIBOSPRAY TCL PTHREADS SILENT
>

here is the mistake. "LINUX" configures for 32-bit. you need "LINUXAMD64"
for a 64-bit configuration.

axel.

from the top of the "configure" script:

# Architectures:
# ---------------------------------------------------------------
# AIX6_64 - compile on an RS/6000 machine (gcc/g++/xlc/xlC)
# ANDROIDARMV7A - cross-compile for Android on ARM V7A
# FREEBSD - compile on a FreeBSD machine (gcc/g++)
# FREEBSDAMD64 - compile on a FreeBSD machine (gcc/g++)
# HPUX11 - compile on an HP-UX 11.0 machine (cc/CC/cc/aCC)
# IRIX6 - compile on an SGI, IRIX 6.X or later, 32-bit ABI
# IRIX6_64 - compile on an SGI, IRIX 6.X or later, 64-bit ABI
# LINUX - compile on a Linux machine (x86 32-bit)
# LINUXAMD64 - compile on a Linux machine (x86 64-bit AMD64 or EM64T)
# LINUXIA64 - compile on a Linux machine (Itanium)
# LINUXALPHA - compile on a Linux machine (Alpha)
# LINUXPPC - compile on a Linux machine (PowerPC)
# LINUXPPC64 - compile on a Linux machine (64-bit PowerPC)
# MACOSX - compile on a MacOS-X PowerPC machine
# MACOSXX86 - compile on a MacOS-X x86 machine, 32-bit ABI
# MACOSXX86_64 - compile on a MacOS-X x86 machine, 64-bit ABI
# TRU64 - compile on a DEC Alpha/Digital Unix 4.0 machine
# SOLARIS2 - compile on a Solaris machine, 32-bit ABI
# SOLARIS2_64 - compile on a Solaris machine, 64-bit ABI
# SOLARISX86 - compile on a Solaris x86 machine
# SOLARISX86_64 - compile on a Solaris x86 machine
# WIN32 - compile on a Win32 machine (NT, 95, 98, etc)
# WIN64 - compile on a Win64 machine (Windows XP x64)

> [ec2-user_at_ip-172-31-18-188 vmd-1.9.4a51]$ ./configure
>
> using configure.options: LINUX MESA FLTK TK ACTC MPI LIBOSPRAY TCL
> PTHREADS SILENT
>
>
>
> Then I followed the steps in the install guide to make the source like
> this:
>
> [ec2-user_at_ip-172 vmd-1.9.4a51]$ cd src
>
> [ec2-user_at_ip-172 src]$ make veryclean
>
> [ec2-user_at_ip-172 src]$ make
>
> Compiling OpenGLDisplayDevice.C --> OpenGLDisplayDevice.o ...
>
> In file included from /usr/include/features.h:447:0,
>
> from
> /usr/include/c++/7/x86_64-redhat-linux/32/bits/os_defines.h:39,
>
> from
> /usr/include/c++/7/x86_64-redhat-linux/32/bits/c++config.h:533,
>
> from /usr/include/c++/7/cstdlib:41,
>
> from /usr/include/c++/7/stdlib.h:36,
>
> from OpenGLDisplayDevice.C:24:
>
> /usr/include/gnu/stubs.h:7:11: fatal error: gnu/stubs-32.h: No such file
> or directory
>
> # include <gnu/stubs-32.h>
>
> ^~~~~~~~~~~~~~~~
>
> compilation terminated.
>
> make: *** [OpenGLDisplayDevice.o] Error 1
>
>
>
> *From:* Axel Kohlmeyer <akohlmey_at_gmail.com>
> *Sent:* Thursday, January 7, 2021 15:14
> *To:* Chris Taylor <christay_at_usc.edu>
> *Cc:* vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: RE: Install VMD from source on Amazon EC2 instance
>
>
>
>
>
>
>
> On Thu, Jan 7, 2021 at 6:10 PM Chris Taylor <christay_at_usc.edu> wrote:
>
> Also, just to be clear I want to build a 64-bit version of VMD. It’s just
> that it seems like it wants to build some part of it using a 32-bit
> library, but I’m not sure why.
>
>
>
> that makes no sense. as already requested, please provide more information
> about the individual steps you did and how you configured VMD to be
> compiled from source.
>
>
>
> axel.
>
>
>
>
>
>
>
> Chris
>
>
>
> *From:* Chris Taylor
> *Sent:* Thursday, January 7, 2021 14:54
> *To:* Axel Kohlmeyer <akohlmey_at_gmail.com>
> *Cc:* vmd-l_at_ks.uiuc.edu
> *Subject:* RE: vmd-l: RE: Install VMD from source on Amazon EC2 instance
>
>
>
> I get this error when I try to compile, and when I looked it up it seems
> to point to the lack of a package like glibc-devel.i686 – the 32bit
> development libs for this version of Linux. The information I’ve found
> online is that Amazon makes 32bit runtime libraries available in their
> version of Linux but not the development libraries. I think it would be
> nice to be able to run VMD on an AWS Amazon Linux2 VM, because I’ve been
> doing some work with their ParallelCluster and it would be cool to run an
> MPI version of VMD.
>
>
> /usr/include/gnu/stubs.h:7:11: fatal error: gnu/stubs-32.h: No such file
> or directory
>
> # include <gnu/stubs-32.h>
>
> ^~~~~~~~~~~~~~~~
>
> compilation terminated.
>
> make: *** [OpenGLDisplayDevice.o] Error 1
>
>
>
> *From:* Axel Kohlmeyer <akohlmey_at_gmail.com>
> *Sent:* Thursday, January 7, 2021 14:49
> *To:* Chris Taylor <christay_at_usc.edu>
> *Cc:* vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: RE: Install VMD from source on Amazon EC2 instance
>
>
>
> why are you trying to build 32-bit binaries in the first place since you
> appear to be running on a 64-bit host?
>
> you need to provide more information about what it is exactly that you
> were doing for people to be able to give meaningful advice.
>
>
>
> axel.
>
>
>
> On Thu, Jan 7, 2021 at 5:34 PM Chris Taylor <christay_at_usc.edu> wrote:
>
> Just wondering if anybody had any ideas for me on this? Maybe there’s a
> compiler directive or option I can give to work around it? Thanks
>
> Chris
>
>
>
> *From:* Chris Taylor
> *Sent:* Monday, January 4, 2021 16:54
> *To:* vmd-l_at_ks.uiuc.edu
> *Subject:* RE: Install VMD from source on Amazon EC2 instance
>
>
>
> I get this error when I try to ‘make’ vmd-1.9.4a51. This is on a Amazon
> Linux2 EC2 instance, and they seem to be saying I can’t download something
> like glibc6-devel.i686 or whatever it is to give me the 32-bit build
> dependencies- they don’t provide those RPMs. I want to try to build from
> source because I want to compile MPI in. Under the circumstances, what are
> my options? Thanks.
>
>
>
> $ make
>
> Compiling OpenGLDisplayDevice.C --> OpenGLDisplayDevice.o ...
>
> In file included from /usr/include/features.h:447:0,
>
> from
> /usr/include/c++/7/x86_64-redhat-linux/32/bits/os_defines.h:39,
>
> from
> /usr/include/c++/7/x86_64-redhat-linux/32/bits/c++config.h:533,
>
> from /usr/include/c++/7/cstdlib:41,
>
> from /usr/include/c++/7/stdlib.h:36,
>
> from OpenGLDisplayDevice.C:24:
>
> /usr/include/gnu/stubs.h:7:11: fatal error: gnu/stubs-32.h: No such file
> or directory
>
> # include <gnu/stubs-32.h>
>
> ^~~~~~~~~~~~~~~~
>
> compilation terminated.
>
> make: *** [OpenGLDisplayDevice.o] Error 1
>
>
>
>
> --
>
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!vVjYaF9bow2wy1BEtdltor1i9ESBhNgqyII5Iszf_UnoGUSE897WJahn8TjaRfrJCw$
> <https://urldefense.com/v3/__http:/goo.gl/1wk0__;!!LIr3w8kk_Xxm!9UZPqf4wCjBs61AbQsteLIZacQY4OZUb-Uj3-jtof3T1JFF0LsmfhsRbyDpj3b0$>
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
>
>
>
> --
>
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!vVjYaF9bow2wy1BEtdltor1i9ESBhNgqyII5Iszf_UnoGUSE897WJahn8TjaRfrJCw$
> <https://urldefense.com/v3/__http:/goo.gl/1wk0__;!!LIr3w8kk_Xxm!5Y5WzptQ1HkJjJRBnxlirQbZqZdebbl0Yd3JGWrRbBY0lmkpZdAKFx20VGnOzuU$>
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!vVjYaF9bow2wy1BEtdltor1i9ESBhNgqyII5Iszf_UnoGUSE897WJahn8TjaRfrJCw$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.