ah, that works too. (if two machines are similar)
Hai
On Tue, Jan 17, 2017 at 10:45 PM, Coleman, Marcus [JRDUS Non-J&J] <
mcolem19.its.jnj.com> wrote:
> That is the thing...all software is installed in the /opt/ directory on
> the identical machine F1 and every other compute node on this network.
>
> I took the easy route and copied the folder over to F2 from F1 "/opt/"
> directory. (gotta Love UNIX)
> I will have the scientist to test in the AM.
>
> Thanks for the all the help!
>
> -----Original Message-----
> From: Hai Nguyen [mailto:nhai.qn.gmail.com]
> Sent: Tuesday, January 17, 2017 7:35 PM
> To: AMBER Mailing List
> Subject: [EXTERNAL] Re: [AMBER] amber16 Centos 7
>
> you must have admin (root) permission to write thing on /opt/ folder
>
> So
>
> cd $HOME
> cp -rf $AMBERHOME .
> cd amber16
> export AMBERHOME=`pwd`
> make distclean
> # serial build
> ./configure gnu
> make install
>
> and so on for parallel (-mpi and -cuda) build.
>
> hope this help.
> Hai
>
> On Tue, Jan 17, 2017 at 10:24 PM, Coleman, Marcus [JRDUS Non-J&J] <
> mcolem19.its.jnj.com> wrote:
>
> > [root.f2 ~]# cd $AMBERHOME
> > [root.f2 amber16]# pwd
> > /opt/amber16
> > [root.f2 amber16]#
> >
> > -----Original Message-----
> > From: Coleman, Marcus [JRDUS Non-J&J]
> > Sent: Tuesday, January 17, 2017 7:23 PM
> > To: AMBER Mailing List
> > Subject: [EXTERNAL] Re: [AMBER] amber16 Centos 7
> >
> > Thanks for the speedy responses!
> >
> > I can copy the previously-installed amber from F1 (which is identical
> > in hardware and software) to this node F2.
> >
> > I use to be a windows guy and coping program folders from one machine
> > to another machine usually causes a foobar...
> >
> > I also have the tar file of amber16....but would not I run into the
> > same issue?
> >
> > That is how all of this started with a amber16.tar...
> >
> >
> >
> >
> > -----Original Message-----
> > From: Hai Nguyen [mailto:nhai.qn.gmail.com]
> > Sent: Tuesday, January 17, 2017 7:17 PM
> > To: AMBER Mailing List
> > Subject: [EXTERNAL] Re: [AMBER] amber16 Centos 7
> >
> > where is your amber folder?
> >
> > The message "Permission denied" means you need to run as root, which
> > is NOT recommended to do so.
> >
> > Can you just either
> > - use a tar file of amber?
> > - copy previous-installed amber to some where else in your $HOME folder?
> >
> > Hai
> >
> > On Tue, Jan 17, 2017 at 10:08 PM, Coleman, Marcus [JRDUS Non-J&J] <
> > mcolem19.its.jnj.com> wrote:
> >
> > > Thanks!
> > >
> > > I ran : "Make distclean" (started over)
> > >
> > > Change to regular user and ran: "./configure -cuda gnu"
> > >
> > > I am getting below error. Any suggestion would be greatly appreciated!
> > >
> > > [mcolem19.f2 amber16]$ ./configure -cuda gnu Checking for updates...
> > > Checking for available patches online. This may take a few seconds...
> > >
> > > Available AmberTools 16 patches:
> > >
> > > No patches available
> > >
> > > Available Amber 16 patches:
> > >
> > > No patches available
> > >
> > > require development version of PythonCompatible Python found! Using
> > > CUDA Version 8.0 detected Configuring for SM2.0, SM3.0, SM5.0,
> > > SM5.2, SM5.3, SM6.0 and SM6.1
> > >
> > > Obtaining the gnu compiler suite versions, e.g.:
> > > gcc -v
> > > The C version is 4.8.5
> > > The Fortran version is 4.8.5
> > > ./configure2: line 2254: testp.c: Permission denied
> > >
> > > Testing the gcc compiler:
> > > gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
> > > testp.c
> > > gcc: error: testp.c: No such file or directory
> > > gcc: fatal error: no input files
> > > compilation terminated.
> > > ./configure2: line 2266: ./testp: No such file or directory
> > > Error: Unable to compile a C program using gcc -fPIC
> > > -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> > > Please check your compiler settings or configure flags.
> > > Configure failed due to the errors above!
> > > [mcolem19.f2 amber16]$
> > >
> > > ####
> > >
> > > [mcolem19.f2 amber16]$ whereis gcc
> > > gcc: /usr/bin/gcc /usr/lib/gcc /usr/libexec/gcc
> > > /usr/share/man/man1/gcc.1.gz
> > >
> > > [mcolem19.f2 amber16]$ gcc --version gcc (GCC) 4.8.5 20150623 (Red
> > > Hat 4.8.5-11) Copyright (C) 2015 Free Software Foundation, Inc.
> > > This is free software; see the source for copying conditions. There
> > > is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A
> > > PARTICULAR
> > PURPOSE.
> > >
> > > [mcolem19.f2 amber16]$ which gcc
> > > /usr/bin/gcc
> > > [mcolem19.f2 amber16]$
> > >
> > >
> > >
> > > -----Original Message-----
> > > From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
> > > Sent: Tuesday, January 17, 2017 4:24 PM
> > > To: AMBER Mailing List
> > > Subject: [EXTERNAL] Re: [AMBER] amber16 Centos 7
> > >
> > > We *strongly* recommend you do not install as root. It shouldn't be
> > > necessary and can potentially open the door to lots of problems.
> > >
> > > As Hai suggested reading the Amber 16 manual section on Installation
> > > may be quite helpful. Another great resource is Jason Swail's wiki
> > > http://jswails.wikidot.com/#toc6.
> > >
> > > -Dan
> > >
> > > On Tue, Jan 17, 2017 at 6:50 PM, Coleman, Marcus [JRDUS Non-J&J] <
> > > mcolem19.its.jnj.com> wrote:
> > > > From: Coleman, Marcus [JRDUS Non-J&J]
> > > > Sent: Tuesday, January 17, 2017 3:47 PM
> > > > To: 'amber.ambermd.org'
> > > > Subject: Amber16 install Centos 7 missing amber 16 tools
> > > >
> > > > Hello
> > > >
> > > >
> > > > I have install Amber 16 on Centos 7
> > > >
> > > > [root.f2 ~]# cat /etc/redhat-release CentOS Linux release 7.3.1611
> > > > (Core)
> > > > [root.f2 ~]# uname -r
> > > > 3.10.0-514.2.2.el7.x86_64
> > > > [root.f2 ~]#
> > > >
> > > >
> > > > [root.f2 amber16]# ./update_amber --update Preparing to apply
> > > > updates... please wait.
> > > > No new updates available for AmberTools 16 No new updates
> > > > available for Amber 16
> > > >
> > > > Amber16 was previously install on an identical machine but not by me.
> > > >
> > > > The issue is /opt/amber16/bin directory is missings tons of files
> > > compared to the other identical machine.
> > > > (see below)
> > > > root.f2 ~]# cd /opt/amber16/bin
> > > > [root.f2 bin]# pwd
> > > > /opt/amber16/bin
> > > > [root.f2 bin]# ls
> > > > ######
> > > > nc-config nccopy ncdump ncgen ncgen3 nf-config pmemd.cuda
> > > > pmemd.cuda_DPFP pmemd.cuda_SPFP pmemd.cuda_SPXP ######
> > > > [root.f2 bin]#
> > > >
> > > >
> > > > [root.f1 ~]# cd /opt/amber16/bin
> > > > [root.f1 bin]# pwd
> > > > /opt/amber16/bin
> > > > [root.f1 bin]# ls
> > > >
> > > > #####
> > > > acdoctor fftw-wisdom-to-conf mmpbsa_py_energy
> > > PdbSearcher.py sgldinfo.sh
> > > > addles fix_new_inpcrd_vel mmpbsa_py_nabnmode
> pmemd
> > > sgldwt.sh
> > > > add_pdb frcmod2xml mm_pbsa_statistics.pl
> > > pmemd.cuda softcore_setup.py
> > > > AddToBox func molsurf
> > > pmemd.cuda_DPFP sqm
> > > > am1bcc gbnsr6 MTKppConstants
> > > pmemd.cuda_SPFP stats
> > > > ambmask hcp_getpdb nab
> > > pmemd.cuda_SPXP stdLib2Sdf
> > > > ambpdb hybrid nab2c
> > > prep2xml superimposer
> > > > antechamber IPMach.py nc-config
> > > prepgen sviol
> > > > ante-MMPBSA.py lmanal nccopy
> > > process_mdout.perl sviol2
> > > > atomtype makeANG_RST ncdump
> > > process_minout.perl teLeap
> > > > bondtype makeCHIR_RST ncgen
> > > PropPDB tinker_to_amber
> > > > capActiveSite makeDIST_RST ncgen3
> > > protonator tleap
> > > > CartHess2FC.py match nef_to_RST
> > > pymdpbsa transform
> > > > charmmgen match_atomname new2oldparm
> > > pytleap translate
> > > > charmmlipid2amber.py matextract new_crd_to_dyn
> > > reduce tss_init
> > > > ChBox matgen new_to_old_crd
> > > residuegen tss_main
> > > > CheckMD matmerge nf-config
> resp
> > > tss_next
> > > > cphstats matmul nfe-umbrella-slice
> > > respgen ucpp
> > > > cpinutil.py MCPB nmode
> > > rism1d UnitCell
> > > > cpptraj MCPB.py OptC4.py
> > > rism3d.orave volslice
> > > > database mdgx paramfit
> > > rism3d.snglpnt xaLeap
> > > > elsize mdnab parmcal
> > > rism3d.thermo xleap
> > > > espgen mdout2pymbar.pl parmchk
> > > sander xparmed
> > > > espgen.py mdout_analyzer.py parmchk2
> > > sander.LES yacc
> > > > fantasian minab parmed
> > saxs_md
> > > > FEW.pl mmE pbsa
> > > saxs_rism
> > > > ffgbsa mm_pbsa.pl pdb4amber
> > > senergy
> > > > fftw-wisdom MMPBSA.py pdbSearcher
> > > sequenceAligner
> > > > #####
> > > > [root.f1 bin]#
> > > >
> > > >
> > > > How can I get all of the files listed above in /opt/amber16/
> > > bin/...thanks..
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> > >
> > > --
> > > -------------------------
> > > Daniel R. Roe
> > > Laboratory of Computational Biology
> > > National Institutes of Health, NHLBI
> > > 5635 Fishers Ln, Rm T900
> > > Rockville MD, 20852
> > > https://www.lobos.nih.gov/lcb
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
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> > AMBER.ambermd.org
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> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Jan 17 2017 - 20:00:05 PST
