From trinh.vo at jpl.nasa.gov Thu Oct 14 21:57:42 2021 From: trinh.vo at jpl.nasa.gov (Vo, Trinh T (US 398K)) Date: Thu, 14 Oct 2021 19:57:42 +0000 Subject: [xcrysden] [EXTERNAL] Re: Problem with installing xcrysden on Mac OS 10.17.7 (Catalina) In-Reply-To: References: <571D0262-E5EA-4E42-8418-04AFDF97A4A4@jpl.nasa.gov> Message-ID: <26F12D65-8496-4084-9B59-EE531BA56BB3@jpl.nasa.gov> Thank you very much. I am sorry for a long delay in response. I have been dragged by other projects and do not have time to work on this until now. I will look at the links you show and work on it to see if it works. Trinh From: on behalf of Gavin Abo Reply-To: XCrySDen mailing list Date: Monday, August 16, 2021 at 9:19 PM To: "xcrysden at democritos.it" Subject: [EXTERNAL] Re: [xcrysden] Problem with installing xcrysden on Mac OS 10.17.7 (Catalina) At [1] , I read Xcode 12 has a new "feature": Clang now reports an error when you use a function without an explicit declaration when building C or Objective-C code for macOS (-Werror=implicit-function-declaration flag is on). This additional error detection unifies Clang?s behavior for iOS/tvOS and macOS 64-bit targets for this diagnostic. (49917738) https://developer.apple.com/documentation/xcode-release-notes/xcode-12-release-notes At [2], I read that gcc might default to clang with homebrew. If that is the case, have you tried change it to use gcc [3]? If that does not resolve the issue, I'm not a Mac user such that I unfortunately cannot be of much help with that. Perhaps, there is a Mac user in the list that will respond if they have solution for that error. [1] https://github.com/astropy/astropy/issues/10770 [2] https://github.com/openvenues/libpostal/issues/511 [3] https://apple.stackexchange.com/questions/245891/installed-gcc-with-homebrew-now-how-to-use-that-gcc-instead-of-clang On 8/16/2021 11:02 AM, Vo, Trinh T (US 398K) wrote: Dear Developer, I compiled from source code of xcrysden on my new laptop, and I encountered the following errors: # Compiling XCRYSDEN C-code # # # #------------------------------# cd C; /Applications/Xcode.app/Contents/Developer/usr/bin/make "TOPDIR=/Users/trinhvo/xcrysden-1.6.2" compile make TOPDIR=/Users/trinhvo/xcrysden-1.6.2 gcc -ffast-math -funroll-loops -fPIC -pedantic -Wall -I/usr/include/tcl8.6 -I/usr/local/Cellar/tcl-tk/8.6.11_1/include -I/usr/local/Cellar/tcl-tk/8.6.11_1/include -c xcAppInit.c xcAppInit.c:407:3: error: implicit declaration of function 'XGetErrorText' is invalid in C99 [-Werror,-Wimplicit-function-declaration] XGetErrorText(display,event->error_code,buffer,sizeof(buffer)-1); ^ xcAppInit.c:1834:7: warning: 'glDrawBuffer' is deprecated: first deprecated in macOS 10.14 - OpenGL API deprecated. (Define GL_SILENCE_DEPRECATION to silence these warnings) [-Wdeprecated-declarations] glDrawBuffer(GL_BACK); I do not know how to fix this error. I have installed all the required libs using homebrew - Tcl/Tk - mesa and mesa-glu - FFTW3 For these libs, I download from web) - BWidget - Togl (2.0 or later). I appreciate if you could help me to fix this error. Thank you very much, Trinh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20211014/89757c5b/attachment.htm From trinh.vo at jpl.nasa.gov Thu Oct 14 21:57:45 2021 From: trinh.vo at jpl.nasa.gov (Vo, Trinh T (US 398K)) Date: Thu, 14 Oct 2021 19:57:45 +0000 Subject: [xcrysden] [EXTERNAL] Re: Problem with installing xcrysden on Mac OS 10.17.7 (Catalina) (Vo, Trinh T) In-Reply-To: References: Message-ID: Dear Prof. Wood, Thank you very much for your message. Yes, in the past I used macports to install Xcrysden. I had conflict with Home Brew. Macports supports a number of software, but some others it does not, and I installed Home Brew to install those software , but then Macports is deactivated. Only one is allowed to be active. I still can use Xcrysden, but for some libraries, they are duplicated in different locations. Therefore, for my new laptop, I intended to compile from source, but then I have other problems. Let me try to work around if I can solve the problem. If not, I will install Macports and then Xcrysden. Thanh you, Trinh ?On 8/18/21, 7:02 PM, "xcrysden-bounces at democritos.it on behalf of dmwood" wrote: Just a reminder that xcrysden can be installed via the macports package manager. In the off chance that readers don?t know about macports: many science-related package are available and build and install painlessly in /opt/local tree. ?DMW dmwood at mines.edu Emeritus Assoc Prof Department of Physics Colorado School of Mines _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it https://urldefense.us/v3/__http://www.democritos.it/mailman/listinfo/xcrysden__;!!PvBDto6Hs4WbVuu7!Yg_BSr7wbCHYA1DpbMT7KtMVdFqaY3G2_E3_XwkOqB98hVTIPsFs4I0wlC4JDc3gAvsk$ From gabo13279 at gmail.com Fri Oct 15 07:21:18 2021 From: gabo13279 at gmail.com (Gavin Abo) Date: Thu, 14 Oct 2021 23:21:18 -0600 Subject: [xcrysden] [EXTERNAL] Re: Problem with installing xcrysden on Mac OS 10.17.7 (Catalina) (Vo, Trinh T) In-Reply-To: References: Message-ID: While it should be better to install XCrySDen directly in your native environment (Mac OS), if your computer hardware has enough resources (hard drive space, etc.) another possible alternative might be to use a virtualization software [1] like qemu [2] in which a Linux distribution could be installed such as Ubuntu and install XCrySDen in that [3]. [1] https://en.wikipedia.org/wiki/Comparison_of_platform_virtualization_software [2] https://www.qemu.org/download/#macos [3] http://www.democritos.it/pipermail/xcrysden/2020-January/001975.html Kind Regards, Gavin On 10/14/2021 1:57 PM, Vo, Trinh T (US 398K) wrote: > Dear Prof. Wood, > > Thank you very much for your message. Yes, in the past I used macports to install Xcrysden. I had conflict with Home Brew. Macports supports a number of software, but some others it does not, and I installed Home Brew to install those software , but then Macports is deactivated. Only one is allowed to be active. I still can use Xcrysden, but for some libraries, they are duplicated in different locations. Therefore, for my new laptop, I intended to compile from source, but then I have other problems. Let me try to work around if I can solve the problem. If not, I will install Macports and then Xcrysden. > > Thanh you, > > Trinh > > ?On 8/18/21, 7:02 PM, "xcrysden-bounces at democritos.it on behalf of dmwood" wrote: > > Just a reminder that xcrysden can be installed via the macports package manager. In the off chance that readers don?t know about macports: many science-related package are available and build and install painlessly in /opt/local tree. > ?DMW > > dmwood at mines.edu > Emeritus Assoc Prof > Department of Physics > Colorado School of Mines From fink at snaggledworks.com Fri Oct 15 11:35:14 2021 From: fink at snaggledworks.com (fink at snaggledworks.com) Date: Fri, 15 Oct 2021 04:35:14 -0500 Subject: [xcrysden] [EXTERNAL] Re: Problem with installing xcrysden on Mac OS 10.17.7 (Catalina) In-Reply-To: <26F12D65-8496-4084-9B59-EE531BA56BB3@jpl.nasa.gov> References: <571D0262-E5EA-4E42-8418-04AFDF97A4A4@jpl.nasa.gov> <26F12D65-8496-4084-9B59-EE531BA56BB3@jpl.nasa.gov> Message-ID: <0ca56f07-95e9-921f-caf4-ba25f8eb427c@snaggledworks.com> On 10/14/21 2:57 PM, Vo, Trinh T (US 398K) wrote: > Thank you very much. I am sorry for a long delay in response. I have been dragged by other projects and do not have time to work on this until now. I will look at the links you show and work on it to see if it works. > > Trinh > > From: on behalf of Gavin Abo > Reply-To: XCrySDen mailing list > Date: Monday, August 16, 2021 at 9:19 PM > To: "xcrysden at democritos.it" > Subject: [EXTERNAL] Re: [xcrysden] Problem with installing xcrysden on Mac OS 10.17.7 (Catalina) > > > At [1] , I read Xcode 12 has a new "feature": > > Clang now reports an error when you use a function without an explicit declaration when building C or Objective-C code for macOS (-Werror=implicit-function-declaration flag is on). This additional error detection unifies Clang?s behavior for iOS/tvOS and macOS 64-bit targets for this diagnostic. (49917738) > > https://developer.apple.com/documentation/xcode-release-notes/xcode-12-release-notes > > At [2], I read that gcc might default to clang with homebrew. If that is the case, have you tried change it to use gcc [3]? > > If that does not resolve the issue, I'm not a Mac user such that I unfortunately cannot be of much help with that. Perhaps, there is a Mac user in the list that will respond if they have solution for that error. > [1] https://github.com/astropy/astropy/issues/10770 > [2] https://github.com/openvenues/libpostal/issues/511 > [3] https://apple.stackexchange.com/questions/245891/installed-gcc-with-homebrew-now-how-to-use-that-gcc-instead-of-clang > On 8/16/2021 11:02 AM, Vo, Trinh T (US 398K) wrote: > Dear Developer, > > I compiled from source code of xcrysden on my new laptop, and I encountered the following errors: > > # Compiling XCRYSDEN C-code # > # # > #------------------------------# > > cd C; /Applications/Xcode.app/Contents/Developer/usr/bin/make "TOPDIR=/Users/trinhvo/xcrysden-1.6.2" compile > make TOPDIR=/Users/trinhvo/xcrysden-1.6.2 > gcc -ffast-math -funroll-loops -fPIC -pedantic -Wall -I/usr/include/tcl8.6 -I/usr/local/Cellar/tcl-tk/8.6.11_1/include -I/usr/local/Cellar/tcl-tk/8.6.11_1/include -c xcAppInit.c > xcAppInit.c:407:3: error: implicit declaration of function 'XGetErrorText' is > invalid in C99 [-Werror,-Wimplicit-function-declaration] > XGetErrorText(display,event->error_code,buffer,sizeof(buffer)-1); > ^ > xcAppInit.c:1834:7: warning: 'glDrawBuffer' is deprecated: first deprecated in > macOS 10.14 - OpenGL API deprecated. (Define GL_SILENCE_DEPRECATION to > silence these warnings) [-Wdeprecated-declarations] > glDrawBuffer(GL_BACK); Implicit declaration errors are due to not including a header declaring that function (this is critical with ARM chips). Homebrew's formula apparently doesn't pull in X11 -I calls, so it's naturally not finding X11/Xlib.h that declares XGetErrorText. A quick glance suggests that their Tcl/TK is Aqua and not X11 based. I've no idea what will happen when X11 based xcrysden interacts with Aqua Tcl/TK. FWIW, Fink's xcrysden builds and works on Catalina and Big Sur. Hanspeter (Fink's xcrysden maintainer) From fink at snaggledworks.com Fri Oct 15 16:42:30 2021 From: fink at snaggledworks.com (fink at snaggledworks.com) Date: Fri, 15 Oct 2021 09:42:30 -0500 Subject: [xcrysden] [EXTERNAL] Re: Problem with installing xcrysden on Mac OS 10.17.7 (Catalina) In-Reply-To: <0ca56f07-95e9-921f-caf4-ba25f8eb427c@snaggledworks.com> References: <571D0262-E5EA-4E42-8418-04AFDF97A4A4@jpl.nasa.gov> <26F12D65-8496-4084-9B59-EE531BA56BB3@jpl.nasa.gov> <0ca56f07-95e9-921f-caf4-ba25f8eb427c@snaggledworks.com> Message-ID: On 2021-10-15 04:35, fink at snaggledworks.com wrote: > On 10/14/21 2:57 PM, Vo, Trinh T (US 398K) wrote: >> Thank you very much. I am sorry for a long delay in response. I have >> been dragged by other projects and do not have time to work on this >> until now. I will look at the links you show and work on it to see >> if it works. >> >> Trinh >> >> From: on behalf of Gavin Abo >> >> Reply-To: XCrySDen mailing list >> Date: Monday, August 16, 2021 at 9:19 PM >> To: "xcrysden at democritos.it" >> Subject: [EXTERNAL] Re: [xcrysden] Problem with installing xcrysden on >> Mac OS 10.17.7 (Catalina) >> >> >> At [1] , I read Xcode 12 has a new "feature": >> >> Clang now reports an error when you use a function without an explicit >> declaration when building C or Objective-C code for macOS >> (-Werror=implicit-function-declaration flag is on). This additional >> error detection unifies Clang?s behavior for iOS/tvOS and macOS 64-bit >> targets for this diagnostic. (49917738) >> >> https://developer.apple.com/documentation/xcode-release-notes/xcode-12-release-notes >> >> At [2], I read that gcc might default to clang with homebrew. If that >> is the case, have you tried change it to use gcc [3]? >> >> If that does not resolve the issue, I'm not a Mac user such that I >> unfortunately cannot be of much help with that. Perhaps, there is a >> Mac user in the list that will respond if they have solution for that >> error. >> [1] >> https://github.com/astropy/astropy/issues/10770 >> [2] >> https://github.com/openvenues/libpostal/issues/511 >> [3] >> https://apple.stackexchange.com/questions/245891/installed-gcc-with-homebrew-now-how-to-use-that-gcc-instead-of-clang >> On 8/16/2021 11:02 AM, Vo, Trinh T (US 398K) wrote: >> Dear Developer, >> >> I compiled from source code of xcrysden on my new laptop, and I >> encountered the following errors: >> >> # Compiling XCRYSDEN C-code # >> # # >> #------------------------------# >> >> cd C; /Applications/Xcode.app/Contents/Developer/usr/bin/make >> "TOPDIR=/Users/trinhvo/xcrysden-1.6.2" compile >> make TOPDIR=/Users/trinhvo/xcrysden-1.6.2 >> gcc -ffast-math -funroll-loops -fPIC -pedantic -Wall >> -I/usr/include/tcl8.6 -I/usr/local/Cellar/tcl-tk/8.6.11_1/include >> -I/usr/local/Cellar/tcl-tk/8.6.11_1/include -c xcAppInit.c >> xcAppInit.c:407:3: error: implicit declaration of function >> 'XGetErrorText' is >> invalid in C99 [-Werror,-Wimplicit-function-declaration] >> XGetErrorText(display,event->error_code,buffer,sizeof(buffer)-1); >> ^ >> xcAppInit.c:1834:7: warning: 'glDrawBuffer' is deprecated: first >> deprecated in >> macOS 10.14 - OpenGL API deprecated. (Define >> GL_SILENCE_DEPRECATION to >> silence these warnings) [-Wdeprecated-declarations] >> glDrawBuffer(GL_BACK); > > Implicit declaration errors are due to not including a header > declaring that function (this is critical with ARM chips). Homebrew's > formula apparently doesn't pull in X11 -I calls, so it's naturally not > finding X11/Xlib.h that declares XGetErrorText. A quick glance > suggests that their Tcl/TK is Aqua and not X11 based. I've no idea > what will happen when X11 based xcrysden interacts with Aqua Tcl/TK. > > FWIW, Fink's xcrysden builds and works on Catalina and Big Sur. Small correction: xcrysden (and FFTW3) currently uses gfortran9, which is currently failing for some Big Sur installs. But it works if transitioned to gfortran11. > Hanspeter > (Fink's xcrysden maintainer) From m.abbasnejad at gmail.com Wed Oct 27 23:00:47 2021 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Thu, 28 Oct 2021 00:30:47 +0330 Subject: [xcrysden] Error in running xcrysden: Exec format error Message-ID: Dear Developers, Hello, I have got a problem running the compiled version of xcrysden. When running the "xcrysden" command, it got the following error: ~/xcrysden-1.6.2-bin-shared/bin/xcrys: Exec format error Any help would be highly appreciated. Thanks in advance. Regards, N.B. I had the previous version of xcrysden before that (I can not remember which version of that), however it was deleted from my computer. -- --------------------------------------------------------- Mohaddeseh Abbasnejad, Assistant Professor of Physics, Faculty of Physics, Shahid Bahonar University of Kerman, Kerman, Iran P.O. Box 76169-133 Tel: +98 34 31322199 Fax: +98 34 33257434 Cellphone: +98 917 731 7514 E-Mail: m.abbasnejad at gmail.com Website: academicstaff.uk.ac.ir/moabbasnejad --------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20211028/6e9e0028/attachment.htm From gabo13279 at gmail.com Thu Oct 28 04:56:34 2021 From: gabo13279 at gmail.com (Gavin Abo) Date: Wed, 27 Oct 2021 20:56:34 -0600 Subject: [xcrysden] Error in running xcrysden: Exec format error In-Reply-To: References: Message-ID: As seen at [1], xcrysden-1.6.2-linux_x86_64-shared.tar.gz is for a Linux distribution [2] that is 64 bit. As seen at [3-4], the "Exec format error" might be from trying to run a 64 bit executable in an operating system that only runs 32 bit executables. You mentioned using a previous version of XCrySDen.? Have you perhaps tried installing XCrySDen with your package manager (e.g., see [5]), tried installing the xc-1.5.24-linux_x86-semishared.tar.gz for 32 bit that is on the webpage at [1], or tried to compile the xcrysden-1.6.2.tar.gz from source [6] to see if one of those works should you be using a Linux distribution that is 32 bit? [1] http://www.xcrysden.org/Download.html [2] https://en.wikipedia.org/wiki/List_of_Linux_distributions [3] https://stackoverflow.com/questions/66970902/getting-the-error-bash-program-cannot-execute-binary-file-exec-format-erro [4] https://askubuntu.com/questions/648555/bash-program-cannot-execute-binary-file-exec-format-error [5] https://howtoinstall.co/en/xcrysden [6] http://www.democritos.it/pipermail/xcrysden/2021-April/002050.html Kind Regards, Gavin XCrySDen user On 10/27/2021 3:00 PM, mohaddeseh abbasnejad wrote: > > Dear Developers, > > Hello, > I have got a problem running the compiled version of xcrysden. > When running the "xcrysden" command, it got the following error: > ~/xcrysden-1.6.2-bin-shared/bin/xcrys: Exec format error > Any help would be highly appreciated. > Thanks in advance. > Regards, > > N.B. I had the previous version of xcrysden before that (I can not > remember which version of that), however it was deleted from my computer. > > > -- > --------------------------------------------------------- > > Mohaddeseh Abbasnejad, > Assistant Professor of Physics, > Faculty of Physics, > Shahid Bahonar University of Kerman, > Kerman, Iran > P.O. Box 76169-133 > Tel: +98 34 31322199 > Fax: +98 34 33257434 > Cellphone: +98 917 731 7514 > E-Mail: m.abbasnejad at gmail.com > Website: academicstaff.uk.ac.ir/moabbasnejad > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20211027/0b27976c/attachment.htm From m.abbasnejad at gmail.com Sat Oct 30 17:37:10 2021 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Sat, 30 Oct 2021 19:07:10 +0330 Subject: [xcrysden] Error in running xcrysden: Exec format error In-Reply-To: References: Message-ID: Dear Gavin, Thank you very much for your helpful comments. I could solve the problem. Regards, Mohaddeseh On Thu, Oct 28, 2021 at 6:26 AM Gavin Abo wrote: > As seen at [1], xcrysden-1.6.2-linux_x86_64-shared.tar.gz is for a Linux > distribution [2] that is 64 bit. > > As seen at [3-4], the "Exec format error" might be from trying to run a 64 > bit executable in an operating system that only runs 32 bit executables. > > You mentioned using a previous version of XCrySDen. Have you perhaps > tried installing XCrySDen with your package manager (e.g., see [5]), tried > installing the xc-1.5.24-linux_x86-semishared.tar.gz for 32 bit that is on > the webpage at [1], or tried to compile the xcrysden-1.6.2.tar.gz from > source [6] to see if one of those works should you be using a Linux > distribution that is 32 bit? > [1] http://www.xcrysden.org/Download.html > [2] https://en.wikipedia.org/wiki/List_of_Linux_distributions > [3] > https://stackoverflow.com/questions/66970902/getting-the-error-bash-program-cannot-execute-binary-file-exec-format-erro > [4] > https://askubuntu.com/questions/648555/bash-program-cannot-execute-binary-file-exec-format-error > [5] https://howtoinstall.co/en/xcrysden > [6] http://www.democritos.it/pipermail/xcrysden/2021-April/002050.html > > Kind Regards, > Gavin > XCrySDen user > > On 10/27/2021 3:00 PM, mohaddeseh abbasnejad wrote: > > > Dear Developers, > > Hello, > I have got a problem running the compiled version of xcrysden. > When running the "xcrysden" command, it got the following error: > ~/xcrysden-1.6.2-bin-shared/bin/xcrys: Exec format error > Any help would be highly appreciated. > Thanks in advance. > Regards, > > N.B. I had the previous version of xcrysden before that (I can not > remember which version of that), however it was deleted from my computer. > > > -- > --------------------------------------------------------- > > Mohaddeseh Abbasnejad, > Assistant Professor of Physics, > Faculty of Physics, > Shahid Bahonar University of Kerman, > Kerman, Iran > P.O. Box 76169-133 > Tel: +98 34 31322199 > Fax: +98 34 33257434 > Cellphone: +98 917 731 7514 > E-Mail: m.abbasnejad at gmail.com > Website: academicstaff.uk.ac.ir/moabbasnejad > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -- --------------------------------------------------------- Mohaddeseh Abbasnejad, Assistant Professor of Physics, Faculty of Physics, Shahid Bahonar University of Kerman, Kerman, Iran P.O. Box 76169-133 Tel: +98 34 31322199 Fax: +98 34 33257434 Cellphone: +98 917 731 7514 E-Mail: m.abbasnejad at gmail.com Website: academicstaff.uk.ac.ir/moabbasnejad --------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20211030/e6635ecd/attachment.htm