Can the Linux executable file be running on the MAC?
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Can the Linux executable file be running on the MAC?
by Chih-Ying Lin
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Hi
I want to install DSSP 1. I go to this website http://swift.cmbi.kun.nl/gv/dssp/ to install the source codes and the Linux executable file "dsspcmbi". I put both the source codes and the executable file "dsspcmbi" in the same document. 2. Type chmod 777 dsspcmbi 3. Type ./dsspcmbi => -bash: ./dsspcmbi: cannot execute binary file What mistake here? Thank you Lin _______________________________________________ MacOSX-admin mailing list MacOSX-admin@... http://www.omnigroup.com/mailman/listinfo/macosx-admin |
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Re: Can the Linux executable file be running on the MAC?
by Jared Earle
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On Sat, Jun 27, 2009 at 7:16 PM, Chih-Ying Lin<chihying2009@...> wrote:
> What mistake here? Mac OSX is not Linux. The mistake is you cannot run Linux binaries. Here's the difference: jearle@blackbook# file /bin/bash /bin/bash: Mach-O universal binary with 2 architectures /bin/bash (for architecture i386): Mach-O executable i386 /bin/bash (for architecture ppc7400): Mach-O executable ppc jearle@blackbook# scp cat5.org:/bin/bash ./ bash 100% 767KB 383.7KB/s 00:02 jearle@blackbook# file bash bash: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared libs), for GNU/Linux 2.6.9, stripped -- Jared Earle :: There is no SPORK jearle@... :: http://jearle.eu Hosting :: http://cat5.org Blog :: http://blog.23x.net _______________________________________________ MacOSX-admin mailing list MacOSX-admin@... http://www.omnigroup.com/mailman/listinfo/macosx-admin |
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Re: Can the Linux executable file be running on the MAC?
by John Musbach-3
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On Sat, Jun 27, 2009 at 2:16 PM, Chih-Ying Lin<chihying2009@...> wrote:
> What mistake here? 1) From your OS X install disc install the compilation utilities 2) Download the dssp source code (ftp://ftp.cmbi.ru.nl/pub/molbio/software/dsspcmbi.zip), extract them from the zip, follow the instructions in the README file More than likely the premade binary was made for the wrong architecture or was linked to libraries not existent in Mac OS X. Since Mac OS X is not a standard unix environment, you usually have to compile everything from source to get it to work if it's not a Mac OS X specific program. Mac OS X also often lacks the prerequisites needed by many of these programs which means that not only will you have to compile the program you want to use, but others as well first. This can typically be taken care of automatically by the likes of utilities such as MacPorts, although dssp does not seem to be in their repository unfortunately so you're on your own for this one. Good luck! -- Best Regards, John Musbach _______________________________________________ MacOSX-admin mailing list MacOSX-admin@... http://www.omnigroup.com/mailman/listinfo/macosx-admin |
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Re: Can the Linux executable file be running on the MAC?
by Chih-Ying Lin
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Hi
There questions here. 1. how do you print out this information ?? jearle@blackbook# file /bin/bash /bin/bash: Mach-O universal binary with 2 architectures /bin/bash (for architecture i386): Mach-O executable i386 /bin/bash (for architecture ppc7400): Mach-O executable ppc jearle@blackbook# scp cat5.org:/bin/bash ./ bash 100% 767KB 383.7KB/s 00:02 jearle@blackbook# file bash bash: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared libs), for GNU/Linux 2.6.9, stripped 2. How can i do if i want to install DSSP on MAC? 3. Can I install DSSP on Fedora 9.0 ?? Thank you Lin On 6/27/09, Jared Earle <jearle@...> wrote: > On Sat, Jun 27, 2009 at 7:16 PM, Chih-Ying Lin<chihying2009@...> wrote: > > What mistake here? > > Mac OSX is not Linux. The mistake is you cannot run Linux binaries. > > Here's the difference: > > jearle@blackbook# file /bin/bash > /bin/bash: Mach-O universal binary with 2 architectures > /bin/bash (for architecture i386): Mach-O executable i386 > /bin/bash (for architecture ppc7400): Mach-O executable ppc > > jearle@blackbook# scp cat5.org:/bin/bash ./ > bash 100% 767KB 383.7KB/s 00:02 > jearle@blackbook# file bash > bash: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for > GNU/Linux 2.6.9, dynamically linked (uses shared libs), for GNU/Linux > 2.6.9, stripped > > > > -- > Jared Earle :: There is no SPORK > jearle@... :: http://jearle.eu > Hosting :: http://cat5.org > Blog :: http://blog.23x.net > MacOSX-admin mailing list MacOSX-admin@... http://www.omnigroup.com/mailman/listinfo/macosx-admin |
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Re: Can the Linux executable file be running on the MAC?
by Jared Earle
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On Sat, Jun 27, 2009 at 7:33 PM, Chih-Ying Lin<chihying2009@...> wrote:
> 1. how do you print out this information ?? > jearle@blackbook# file /bin/bash > /bin/bash: Mach-O universal binary with 2 architectures > /bin/bash (for architecture i386): Mach-O executable i386 > /bin/bash (for architecture ppc7400): Mach-O executable ppc In terminal, type "file" and the path to the file. > 2. How can i do if i want to install DSSP on MAC? Build from source. > 3. Can I install DSSP on Fedora 9.0 ?? Probably. This is a MacOSX list though. -- Jared Earle :: There is no SPORK jearle@... :: http://jearle.eu Hosting :: http://cat5.org Blog :: http://blog.23x.net _______________________________________________ MacOSX-admin mailing list MacOSX-admin@... http://www.omnigroup.com/mailman/listinfo/macosx-admin |
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Re: Can the Linux executable file be running on the MAC?
by Chih-Ying Lin
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Hi
I follow your instruction. 1. Download the dssp source code (ftp://ftp.cmbi.ru.nl/pub/molbio/software/dsspcmbi.zip), extract them from the zip, follow the instructions in the README file 2. Type => ./DsspCompileCC It shows => Running script to compile the CMBI version of DSSP, please wait... Type dsspcmbi PDBSourcefile DSSPDestinationfile to run the program... => i think the compiling procedure is succesful. 3. Type => dsspcmbi 6LYZ.pdb -bash: /Users/chih-yinglin/DSSP/dsspcmbi: cannot execute binary file What is the problem now? Thank you Lin On 6/27/09, John Musbach <johnmusbach1@...> wrote: > On Sat, Jun 27, 2009 at 2:16 PM, Chih-Ying Lin<chihying2009@...> wrote: > > What mistake here? > > > 1) From your OS X install disc install the compilation utilities > 2) Download the dssp source code > (ftp://ftp.cmbi.ru.nl/pub/molbio/software/dsspcmbi.zip), extract them > from the zip, follow the instructions in the README file > > More than likely the premade binary was made for the wrong > architecture or was linked to libraries not existent in Mac OS X. > Since Mac OS X is not a standard unix environment, you usually have to > compile everything from source to get it to work if it's not a Mac OS > X specific program. Mac OS X also often lacks the prerequisites needed > by many of these programs which means that not only will you have to > compile the program you want to use, but others as well first. This > can typically be taken care of automatically by the likes of utilities > such as MacPorts, although dssp does not seem to be in their > repository unfortunately so you're on your own for this one. Good > luck! > > > -- > Best Regards, > > > John Musbach > MacOSX-admin mailing list MacOSX-admin@... http://www.omnigroup.com/mailman/listinfo/macosx-admin |
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Re: Can the Linux executable file be running on the MAC?
by John Musbach-3
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On Sat, Jun 27, 2009 at 3:06 PM, Chih-Ying Lin<chihying2009@...> wrote:
> 3. Type => dsspcmbi 6LYZ.pdb > > -bash: /Users/chih-yinglin/DSSP/dsspcmbi: cannot execute binary file > > > What is the problem now? One thing I did notice which seemed kind of odd is that among the source code there appears to already be a binary there. Try deleting the DSSP folder, re-extracting from the zip, and before compiling remove the premade binary. Hopefully it'll work this time around. :) -- Best Regards, John Musbach _______________________________________________ MacOSX-admin mailing list MacOSX-admin@... http://www.omnigroup.com/mailman/listinfo/macosx-admin |
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Re: Can the Linux executable file be running on the MAC?
by Jared Earle
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On Sat, Jun 27, 2009 at 8:06 PM, Chih-Ying Lin<chihying2009@...> wrote:
> Hi > I follow your instruction. > 1. Download the dssp source code > (ftp://ftp.cmbi.ru.nl/pub/molbio/software/dsspcmbi.zip), extract them > from the zip, follow the instructions in the README file > > 2. Type => ./DsspCompileCC > It shows => > Running script to compile the CMBI version of DSSP, please wait... > Type dsspcmbi PDBSourcefile DSSPDestinationfile to run the program... > => i think the compiling procedure is succesful. > > 3. Type => dsspcmbi 6LYZ.pdb > > -bash: /Users/chih-yinglin/DSSP/dsspcmbi: cannot execute binary file > > > What is the problem now? You're doing it wrong. jearle@blackbook# curl -sO ftp://ftp.cmbi.ru.nl/pub/molbio/software/dsspcmbi.zip jearle@blackbook# unzip -q dsspcmbi.zip jearle@blackbook# cd dssp jearle@blackbook# ./DsspCompileCC Running script to compile the CMBI version of DSSP, please wait... Type dsspcmbi PDBSourcefile DSSPDestinationfile to run the program... jearle@blackbook# ./dsspcmbi COPYRIGHT W. Kabsch, C. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995 CMBI version by Elmar.Krieger@... / April 4, 2006 USAGE ./dsspcmbi [Options] PDB_File DSSP_File -> Read PDB_File and write DSSP_File ./dsspcmbi [Options] -- dssp_file -> Read from stdin and write DSSP_File ./dsspcmbi -h -> Display this help screen OPTIONS -na Disables the calculation of accessible surface. -c Classic (old) format. -w Wide 2002 format (for future use,not the current standard). -v Verbose. -- Read from standard input. -h -? Prints a help message. -V Prints version, as in first line of the output. ADDITIONAL OPTIONS CONTRIBUTED BY DSSP USERS By Emmanuel.Courcelle@... -ssa Adds information about disulfide bonds to output file -x Renames residues with incomplete sidechains to 'X' -alt2 Keeps an additional AltLoc indicator at the line ends -- Jared Earle :: There is no SPORK jearle@... :: http://jearle.eu Hosting :: http://cat5.org Blog :: http://blog.23x.net _______________________________________________ MacOSX-admin mailing list MacOSX-admin@... http://www.omnigroup.com/mailman/listinfo/macosx-admin |
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Re: Can the Linux executable file be running on the MAC?
by LuKreme
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On 27-Jun-2009, at 13:15, Jared Earle wrote:
>> 3. Type => dsspcmbi 6LYZ.pdb >> >> -bash: /Users/chih-yinglin/DSSP/dsspcmbi: cannot execute binary file >> >> >> What is the problem now? > > You're doing it wrong. He still has that bad linux ELF binary installed. -- One by one the bulbs burned out, like long lives come to their expected ends. _______________________________________________ MacOSX-admin mailing list MacOSX-admin@... http://www.omnigroup.com/mailman/listinfo/macosx-admin |
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Re: Can the Linux executable file be running on the MAC?
by Chih-Ying Lin
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Hi
Thanks a lot ! 1. After compiling, the two following files are created. dsspcmbi dsspcmbi.exe 2. The path of the DSSP file is /usr/local/bin/DSSP. Both dsspcmbi and dsspcmbi.exe are in the file /usr/local/bin/DSSP. 3. So, the last step i type the command in my .profile. setenv dssp /usr/local/bin/DSSP export dssp= /usr/local/bin/DSSP export PATH=$PATH:$DSSP Is it correct ? 4. I also have Gromacs in my MAC. And I type the following command. do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc secondary-structure.xvg For running 5 minutes, the following files are created and DSSP keep running. Is anything wrong here? dd0JIeYC dd2n5lZ5 dd6Lt1VG ddCKhtbw ddH0Kx1A ddH1OHJw ddH7I7Jq ddHu6YEP ddMHmy3S ddOKw3Hm ddORkwCw ddZmd6yo ddfQILug ddfk4Z93 ddhKugF3 ddiE75mM ddk2Smm9 ddnfIvcP ddrcPgKr ddumjJA5 ddv9BjJk ddw1Q7xl Thank you Lin On 6/27/09, Jared Earle <jearle@...> wrote: > On Sat, Jun 27, 2009 at 8:06 PM, Chih-Ying Lin<chihying2009@...> wrote: > > Hi > > I follow your instruction. > > 1. Download the dssp source code > > (ftp://ftp.cmbi.ru.nl/pub/molbio/software/dsspcmbi.zip), extract them > > from the zip, follow the instructions in the README file > > > > 2. Type => ./DsspCompileCC > > It shows => > > Running script to compile the CMBI version of DSSP, please wait... > > Type dsspcmbi PDBSourcefile DSSPDestinationfile to run the program... > > => i think the compiling procedure is succesful. > > > > 3. Type => dsspcmbi 6LYZ.pdb > > > > -bash: /Users/chih-yinglin/DSSP/dsspcmbi: cannot execute binary file > > > > > > What is the problem now? > > > You're doing it wrong. > > jearle@blackbook# curl -sO ftp://ftp.cmbi.ru.nl/pub/molbio/software/dsspcmbi.zip > jearle@blackbook# unzip -q dsspcmbi.zip > jearle@blackbook# cd dssp > jearle@blackbook# ./DsspCompileCC > > Running script to compile the CMBI version of DSSP, please wait... > Type dsspcmbi PDBSourcefile DSSPDestinationfile to run the program... > > jearle@blackbook# ./dsspcmbi > COPYRIGHT > W. Kabsch, C. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995 > CMBI version by Elmar.Krieger@... / April 4, 2006 > USAGE > ./dsspcmbi [Options] PDB_File DSSP_File -> Read PDB_File and write DSSP_File > ./dsspcmbi [Options] -- dssp_file -> Read from stdin and write DSSP_File > ./dsspcmbi -h -> Display this help screen > OPTIONS > -na Disables the calculation of accessible surface. > -c Classic (old) format. > -w Wide 2002 format (for future use,not the current standard). > -v Verbose. > -- Read from standard input. > > -h -? Prints a help message. > -V Prints version, as in first line of the output. > ADDITIONAL OPTIONS CONTRIBUTED BY DSSP USERS > By Emmanuel.Courcelle@... > -ssa Adds information about disulfide bonds to output file > -x Renames residues with incomplete sidechains to 'X' > -alt2 Keeps an additional AltLoc indicator at the line ends > > > > -- > Jared Earle :: There is no SPORK > jearle@... :: http://jearle.eu > Hosting :: http://cat5.org > Blog :: http://blog.23x.net > MacOSX-admin mailing list MacOSX-admin@... http://www.omnigroup.com/mailman/listinfo/macosx-admin |
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Re: Can the Linux executable file be running on the MAC?
by Dan Shoop
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On Jun 27, 2009, at 2:33 PM, John Musbach wrote: > Since Mac OS X is not a standard unix environment Actually Mac OS X *is* a standard unix, and in fact has been certified to be such: http://arstechnica.com/apple/news/2007/08/mac-os-x-leopard-receives-unix-03-certification.ars > , you usually have to > compile everything from source to get it to work if it's not a Mac OS > X specific program. Something you have to do on all the other unices too. Expecting a Linux executable to run on another OS is like expecting a OpenBSD binary to run on Linux. Mac OS X isn't Solaris where you can just take a Linux binary and run it. -d ------------------------------------------------------------------------ Dan Shoop Computer Scientist shoop@... GoogleVoice: 1-646-402-5293 aim: iWiring twitter: @colonelmode _______________________________________________ MacOSX-admin mailing list MacOSX-admin@... http://www.omnigroup.com/mailman/listinfo/macosx-admin |
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