[ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5
-- Forwarded message -- From: wu donghui wdh0...@gmail.com Date: Mon, Mar 3, 2014 at 7:07 PM Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5 To: Marcin Wojdyr marcin.woj...@diamond.ac.uk Dear Marcin, Yes, I set CC=gcc-4.2.1 in cj.rc file or type in command line. As is shown, it can identify gcc for gcc-4.2.1 checking for gcc... gcc-4.2.1 checking whether the C compiler works... no But indicating that the C compiler does not work. I will try Fortran compiler shortly and let you know. Best, Donghui On Mon, Mar 3, 2014 at 5:43 PM, Marcin Wojdyr marcin.woj...@diamond.ac.ukwrote: On Mon, Mar 03, 2014 at 01:16:37PM +0800, wu donghui wrote: gcc version in my Mac OS X 10.8.5 is as below. Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) That's Apple compiler. It supports C and C++ but not Fortran, so you also need a Fortran compiler such as gfortran. checking for gcc... gcc-4.2.1 checking whether the C compiler works... no Did you set CC=gcc-4.2.1? Marcin -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5
Hi If trying to build on Macs (OSX 10.5 - 10.9) I strongly recommend installing either the High Performance Computing gcc/gfortran or investing in the Intel Compilers. http://hpc.sourceforge.net/ http://software.intel.com/en-us/intel-compilers (if you have ) Performance-wise, there's not much to choose between them these days. Clang just doesn't cut the mustard, and rolling your own compilers from the gcc archive can be fraught with difficulty and lead to incorrectly functioning compilers. On 3 Mar 2014, at 11:08, wu donghui wrote: -- Forwarded message -- From: wu donghui wdh0...@gmail.com Date: Mon, Mar 3, 2014 at 7:07 PM Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5 To: Marcin Wojdyr marcin.woj...@diamond.ac.uk Dear Marcin, Yes, I set CC=gcc-4.2.1 in cj.rc file or type in command line. As is shown, it can identify gcc for gcc-4.2.1 checking for gcc... gcc-4.2.1 checking whether the C compiler works… no But indicating that the C compiler does not work. I will try Fortran compiler shortly and let you know. Best, Donghui On Mon, Mar 3, 2014 at 5:43 PM, Marcin Wojdyr marcin.woj...@diamond.ac.uk wrote: On Mon, Mar 03, 2014 at 01:16:37PM +0800, wu donghui wrote: gcc version in my Mac OS X 10.8.5 is as below. Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) That's Apple compiler. It supports C and C++ but not Fortran, so you also need a Fortran compiler such as gfortran. checking for gcc... gcc-4.2.1 checking whether the C compiler works... no Did you set CC=gcc-4.2.1? Marcin -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
[ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5
-- Forwarded message -- From: wu donghui wdh0...@gmail.com Date: Mon, Mar 3, 2014 at 10:44 PM Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5 To: Marcin Wojdyr woj...@gmail.com Dear Marcin, The reason that I want to build from source is that running ipmosflm can not be done from binary code, while binary code only supports imosflm running. Thanks. Best, Donghui On Mon, Mar 3, 2014 at 8:09 PM, Marcin Wojdyr woj...@gmail.com wrote: Yes, I set CC=gcc-4.2.1 in cj.rc file or type in command line. As is shown, it can identify gcc for gcc-4.2.1 checking for gcc... gcc-4.2.1 checking whether the C compiler works... no To me it looks that you set compiler to non-existent gcc-4.2.1, so it doesn't work. Do you have a reason to build CCP4 from source? There are binaries available for OSX. Best regards Marcin
Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Donghui, did you already take a look into config.log to read the error message why your gcc-compiler does not work? You should start at the end of the log file and scroll backwards until you find the error message. Best, Tim On 03/03/2014 03:51 PM, wu donghui wrote: -- Forwarded message -- From: wu donghui wdh0...@gmail.com Date: Mon, Mar 3, 2014 at 10:44 PM Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5 To: Marcin Wojdyr woj...@gmail.com Dear Marcin, The reason that I want to build from source is that running ipmosflm can not be done from binary code, while binary code only supports imosflm running. Thanks. Best, Donghui On Mon, Mar 3, 2014 at 8:09 PM, Marcin Wojdyr woj...@gmail.com wrote: Yes, I set CC=gcc-4.2.1 in cj.rc file or type in command line. As is shown, it can identify gcc for gcc-4.2.1 checking for gcc... gcc-4.2.1 checking whether the C compiler works... no To me it looks that you set compiler to non-existent gcc-4.2.1, so it doesn't work. Do you have a reason to build CCP4 from source? There are binaries available for OSX. Best regards Marcin - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTFJl9UxlJ7aRr7hoRAo/PAJwLSzdU2Undrc0tosdeSSpdC1aSxACgvzUP khM2NeDGueN6Saat/3kZ+iU= =Z6Ci -END PGP SIGNATURE-
Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5
Hi I think you must be doing something wrong if you can't run Mosflm from the ccp4 binary install - it runs for me. How are you trying to run it? If you need the compilers to build Mosflm then I *very* strongly recommend using the compilers I mentioned in my earlier e-mail - they are what the developers of Mosflm (i.e. Andrew Leslie and me) use to build the distribution versions. If you don't have them installed, and you need to build the Mosflm executable, then you should certainly install them. On OSX, installing the HPC compilers is a doddle. However, my even stronger recommendation is to use the executables that we build here in Cambridge - they have been built and tested rigorously, and I don't think you will gain anything from building yourself (apart from maybe a headache...). On 3 Mar 2014, at 14:51, wu donghui wrote: -- Forwarded message -- From: wu donghui wdh0...@gmail.com Date: Mon, Mar 3, 2014 at 10:44 PM Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5 To: Marcin Wojdyr woj...@gmail.com Dear Marcin, The reason that I want to build from source is that running ipmosflm can not be done from binary code, while binary code only supports imosflm running. Thanks. Best, Donghui On Mon, Mar 3, 2014 at 8:09 PM, Marcin Wojdyr woj...@gmail.com wrote: Yes, I set CC=gcc-4.2.1 in cj.rc file or type in command line. As is shown, it can identify gcc for gcc-4.2.1 checking for gcc... gcc-4.2.1 checking whether the C compiler works… no To me it looks that you set compiler to non-existent gcc-4.2.1, so it doesn't work. Do you have a reason to build CCP4 from source? There are binaries available for OSX. Best regards Marcin Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5
BTW, we got one report from a sysadmin who has built ccp4 using Clang (Apple compiler 5.0) + gfortran 4.8 from: http://gcc.gnu.org/wiki/GFortranBinaries#MacOS So it's likely that at least one lab is using CCP4 built with Clang. I'm not aware of any benchmarks, though. Marcin On Mon, Mar 03, 2014 at 12:04:20PM +, Harry Powell wrote: Hi If trying to build on Macs (OSX 10.5 - 10.9) I strongly recommend installing either the High Performance Computing gcc/gfortran or investing in the Intel Compilers. http://hpc.sourceforge.net/ http://software.intel.com/en-us/intel-compilers (if you have ) Performance-wise, there's not much to choose between them these days. Clang just doesn't cut the mustard, and rolling your own compilers from the gcc archive can be fraught with difficulty and lead to incorrectly functioning compilers. On 3 Mar 2014, at 11:08, wu donghui wrote: -- Forwarded message -- From: wu donghui wdh0...@gmail.com Date: Mon, Mar 3, 2014 at 7:07 PM Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5 To: Marcin Wojdyr marcin.woj...@diamond.ac.uk Dear Marcin, Yes, I set CC=gcc-4.2.1 in cj.rc file or type in command line. As is shown, it can identify gcc for gcc-4.2.1 checking for gcc... gcc-4.2.1 checking whether the C compiler works… no But indicating that the C compiler does not work. I will try Fortran compiler shortly and let you know. Best, Donghui On Mon, Mar 3, 2014 at 5:43 PM, Marcin Wojdyr marcin.woj...@diamond.ac.uk wrote: On Mon, Mar 03, 2014 at 01:16:37PM +0800, wu donghui wrote: gcc version in my Mac OS X 10.8.5 is as below. Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) That's Apple compiler. It supports C and C++ but not Fortran, so you also need a Fortran compiler such as gfortran. checking for gcc... gcc-4.2.1 checking whether the C compiler works... no Did you set CC=gcc-4.2.1? Marcin -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5
Dear Tim, Here I attached the config.log file for your help. I have tried to use either gcc-4.2.1 (Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1), or g++-4.2.1(/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1) or gfortran-4.8.1 compiler. Still same error appeared as attached from the config.log file. Thanks for your attention. Best, Donghui On Mon, Mar 3, 2014 at 11:02 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Donghui, did you already take a look into config.log to read the error message why your gcc-compiler does not work? You should start at the end of the log file and scroll backwards until you find the error message. Best, Tim On 03/03/2014 03:51 PM, wu donghui wrote: -- Forwarded message -- From: wu donghui wdh0...@gmail.com Date: Mon, Mar 3, 2014 at 10:44 PM Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5 To: Marcin Wojdyr woj...@gmail.com Dear Marcin, The reason that I want to build from source is that running ipmosflm can not be done from binary code, while binary code only supports imosflm running. Thanks. Best, Donghui On Mon, Mar 3, 2014 at 8:09 PM, Marcin Wojdyr woj...@gmail.com wrote: Yes, I set CC=gcc-4.2.1 in cj.rc file or type in command line. As is shown, it can identify gcc for gcc-4.2.1 checking for gcc... gcc-4.2.1 checking whether the C compiler works... no To me it looks that you set compiler to non-existent gcc-4.2.1, so it doesn't work. Do you have a reason to build CCP4 from source? There are binaries available for OSX. Best regards Marcin - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTFJl9UxlJ7aRr7hoRAo/PAJwLSzdU2Undrc0tosdeSSpdC1aSxACgvzUP khM2NeDGueN6Saat/3kZ+iU= =Z6Ci -END PGP SIGNATURE- config.log Description: Binary data
Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5
On Tuesday, 04 March 2014 01:33:58 PM wu donghui wrote: Dear Tim, Here I attached the config.log file for your help. I have tried to use either gcc-4.2.1 (Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1), or g++-4.2.1(/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1) or gfortran-4.8.1 compiler. Still same error appeared as attached from the config.log file. Thanks for your attention. Looks like either you do not have the g++ compiler completely installed, or it's installed some place the configure script doesn't know about. Does it work to compile something using gcc-4.2.1 directly from the command line? If not then you need to get that working first. If it does work, then you need to figure out which of the environmental variables in your interactive session need to be added also to the ccp4 setup script. Note that it's not finding gcc for the C compiles either. It's using the Apple compiler. Ethan Best, Donghui On Mon, Mar 3, 2014 at 11:02 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Donghui, did you already take a look into config.log to read the error message why your gcc-compiler does not work? You should start at the end of the log file and scroll backwards until you find the error message. Best, Tim On 03/03/2014 03:51 PM, wu donghui wrote: -- Forwarded message -- From: wu donghui wdh0...@gmail.com Date: Mon, Mar 3, 2014 at 10:44 PM Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5 To: Marcin Wojdyr woj...@gmail.com Dear Marcin, The reason that I want to build from source is that running ipmosflm can not be done from binary code, while binary code only supports imosflm running. Thanks. Best, Donghui On Mon, Mar 3, 2014 at 8:09 PM, Marcin Wojdyr woj...@gmail.com wrote: Yes, I set CC=gcc-4.2.1 in cj.rc file or type in command line. As is shown, it can identify gcc for gcc-4.2.1 checking for gcc... gcc-4.2.1 checking whether the C compiler works... no To me it looks that you set compiler to non-existent gcc-4.2.1, so it doesn't work. Do you have a reason to build CCP4 from source? There are binaries available for OSX. Best regards Marcin - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTFJl9UxlJ7aRr7hoRAo/PAJwLSzdU2Undrc0tosdeSSpdC1aSxACgvzUP khM2NeDGueN6Saat/3kZ+iU= =Z6Ci -END PGP SIGNATURE-