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
> >
> _______________________________________________
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>
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>
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>
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Received on Tue Jan 17 2017 - 20:00:02 PST
