From 58ee0085d50fcdc9bfac65a2cd21cc5698ad860d Mon Sep 17 00:00:00 2001 From: Yann Dupont Date: Fri, 3 Feb 2023 16:13:04 +0100 Subject: [PATCH 1/9] add recent zabbix lts --- glicid/packages/monitoring.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 glicid/packages/monitoring.scm diff --git a/glicid/packages/monitoring.scm b/glicid/packages/monitoring.scm new file mode 100644 index 0000000..de6875a --- /dev/null +++ b/glicid/packages/monitoring.scm @@ -0,0 +1,28 @@ +(define-module (glicid packages monitoring) + #:use-module (guix packages) + #:use-module (guix utils) + + #:use-module ((gnu packages monitoring) + #:prefix gnu:) + #:use-module (guix download)) + +; guix defined openconnect is now newer + +(define-public zabbix-server + (package + (inherit gnu:zabbix-server) + (version "6.0.13") + (source + + (origin + (method url-fetch) + (uri (string-append + "https://cdn.zabbix.com/zabbix/sources/stable/" + (version-major+minor version) "/zabbix-" version ".tar.gz")) + (sha256 + (base32 "0d9aws19rvmsrhkvihnwmr4r1drhl20v9lppdw5wjacp7377xqdy")) + + ) +) +) +) From 5c1d4adb186947ed4fef5c26e6f42b4a85fee000 Mon Sep 17 00:00:00 2001 From: Yann Dupont Date: Fri, 3 Feb 2023 17:08:21 +0100 Subject: [PATCH 2/9] test --- glicid/packages/monitoring.scm | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/glicid/packages/monitoring.scm b/glicid/packages/monitoring.scm index de6875a..1eca1ca 100644 --- a/glicid/packages/monitoring.scm +++ b/glicid/packages/monitoring.scm @@ -6,7 +6,21 @@ #:prefix gnu:) #:use-module (guix download)) -; guix defined openconnect is now newer +(define-public zabbix-agentd + (package + (inherit gnu:zabbix-server) + (version "6.0.13") + (source + + (origin + (method url-fetch) + (uri (string-append + "https://cdn.zabbix.com/zabbix/sources/stable/" + (version-major+minor version) "/zabbix-" version ".tar.gz")) + (sha256 + (base32 "0d9aws19rvmsrhkvihnwmr4r1drhl20v9lppdw5wjacp7377xqdy")) +)))) + (define-public zabbix-server (package From d3e06217d3ae041957bd451ae63de33109c52341 Mon Sep 17 00:00:00 2001 From: Yann Dupont Date: Fri, 3 Feb 2023 17:31:40 +0100 Subject: [PATCH 3/9] complete zabbix-server, agent, agent2, cli --- glicid/packages/monitoring.scm | 33 ++++++++++++++++++++++++++++++++- 1 file changed, 32 insertions(+), 1 deletion(-) diff --git a/glicid/packages/monitoring.scm b/glicid/packages/monitoring.scm index 1eca1ca..2967fe8 100644 --- a/glicid/packages/monitoring.scm +++ b/glicid/packages/monitoring.scm @@ -8,7 +8,38 @@ (define-public zabbix-agentd (package - (inherit gnu:zabbix-server) + (inherit gnu:zabbix-agentd) + (version "6.0.13") + (source + + (origin + (method url-fetch) + (uri (string-append + "https://cdn.zabbix.com/zabbix/sources/stable/" + (version-major+minor version) "/zabbix-" version ".tar.gz")) + (sha256 + (base32 "0d9aws19rvmsrhkvihnwmr4r1drhl20v9lppdw5wjacp7377xqdy")) +)))) + + +(define-public zabbix-agent2 + (package + (inherit gnu:zabbix-agent2) + (version "6.0.13") + (source + + (origin + (method url-fetch) + (uri (string-append + "https://cdn.zabbix.com/zabbix/sources/stable/" + (version-major+minor version) "/zabbix-" version ".tar.gz")) + (sha256 + (base32 "0d9aws19rvmsrhkvihnwmr4r1drhl20v9lppdw5wjacp7377xqdy")) +)))) + +(define-public zabbix-cli + (package + (inherit gnu:zabbix-cli) (version "6.0.13") (source From 35b45ccf1c5dcf7c655eaebf84e5fdf7b9b32e4c Mon Sep 17 00:00:00 2001 From: Yann Dupont Date: Fri, 3 Feb 2023 17:47:19 +0100 Subject: [PATCH 4/9] zabbix-cli is NOT the same source --- glicid/packages/monitoring.scm | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/glicid/packages/monitoring.scm b/glicid/packages/monitoring.scm index 2967fe8..8974d04 100644 --- a/glicid/packages/monitoring.scm +++ b/glicid/packages/monitoring.scm @@ -37,21 +37,6 @@ (base32 "0d9aws19rvmsrhkvihnwmr4r1drhl20v9lppdw5wjacp7377xqdy")) )))) -(define-public zabbix-cli - (package - (inherit gnu:zabbix-cli) - (version "6.0.13") - (source - - (origin - (method url-fetch) - (uri (string-append - "https://cdn.zabbix.com/zabbix/sources/stable/" - (version-major+minor version) "/zabbix-" version ".tar.gz")) - (sha256 - (base32 "0d9aws19rvmsrhkvihnwmr4r1drhl20v9lppdw5wjacp7377xqdy")) -)))) - (define-public zabbix-server (package From 0d6ac3c47d79777a231230be4370999c422fcb26 Mon Sep 17 00:00:00 2001 From: Yann Dupont Date: Fri, 3 Feb 2023 18:07:02 +0100 Subject: [PATCH 5/9] add gromacs+gpu. very basic for the moment --- glicid/packages/chemistry.scm | 79 +++++++++++++++++++++++++++++++++++ 1 file changed, 79 insertions(+) create mode 100644 glicid/packages/chemistry.scm diff --git a/glicid/packages/chemistry.scm b/glicid/packages/chemistry.scm new file mode 100644 index 0000000..e7071cb --- /dev/null +++ b/glicid/packages/chemistry.scm @@ -0,0 +1,79 @@ +(define-module (glicid packages chemistry) + #:use-module (guix packages) + #:use-module (guix download) + +#:use-module (guix packages) +#:use-module (guix download) +#:use-module (guix gexp) +#:use-module (guix utils) +#:use-module (guix build-system cmake) +#:use-module ((guix licenses) #:prefix license:) +#:use-module (gnu packages) +#:use-module (gnu packages algebra) +#:use-module (gnu packages mpi) +#:use-module (gnu packages maths) +#:use-module (gnu packages perl) +#:use-module (gnu packages xml) +#:use-module (gnu packages chemistry) +#:use-module (gnu packages documentation) +#:use-module (gnu packages graphviz) +#:use-module (gnu packages pkg-config) +#:use-module (gnu packages python) +#:use-module (gnu packages python-xyz) +#:use-module (gnu packages sphinx) +#:use-module (gnu packages check) +#:use-module (gnu packages gcc) +#:use-module (non-free cuda)) + +(define-public gromacs+cuda + (package + (inherit gromacs) + (arguments + (list #:configure-flags + #~(list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests + ;; Unbundling + "-DGMX_USE_LMFIT=EXTERNAL" + "-DGMX_BUILD_OWN_FFTW=off" + "-DGMX_EXTERNAL_BLAS=on" + "-DGMX_EXTERNAL_LAPACK=on" + "-DGMX_EXTERNAL_TNG=on" + "-DGMX_EXTERNAL_ZLIB=on" + "-DGMX_GPU=CUDA" + (string-append "-DCUDA_TOOLKIT_ROOT_DIR=" #$(this-package-input "cuda-toolkit")) + "-DGMX_EXTERNAL_TINYXML2=on" + (string-append "-DTinyXML2_DIR=" + #$(this-package-input "tinyxml2")) + ;; Workaround for cmake/FindSphinx.cmake version parsing that does + ;; not understand the guix-wrapped `sphinx-build --version' answer + (string-append "-DSPHINX_EXECUTABLE_VERSION=" + #$(package-version python-sphinx))) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fixes + (lambda* (#:key inputs #:allow-other-keys) + ;; Still bundled: part of gromacs, source behind registration + ;; but free software anyways + ;;(delete-file-recursively "src/external/vmd_molfile") + ;; Still bundled: threads-based OpenMPI-compatible fallback + ;; designed to be bundled like that + ;;(delete-file-recursively "src/external/thread_mpi") + ;; Unbundling + (delete-file-recursively "src/external/lmfit") + (delete-file-recursively "src/external/clFFT") + (delete-file-recursively "src/external/fftpack") + (delete-file-recursively "src/external/build-fftw") + (delete-file-recursively "src/external/tng_io") + (delete-file-recursively "src/external/tinyxml2") + (delete-file-recursively "src/external/googletest") + (copy-recursively #$(package-source googletest) + "src/external/googletest") + ;; This test warns about the build host hardware, disable + (substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp" + (("TEST\\(HardwareTopologyTest, HwlocExecute\\)") + "void __guix_disabled()"))))))) + + (propagated-inputs + (modify-inputs (package-propagated-inputs gromacs) + (append cuda hwloc)))) +) + From 71d99ba0dd27e751a16af9fa95f767adfee8f9be Mon Sep 17 00:00:00 2001 From: Yann Dupont Date: Fri, 3 Feb 2023 18:20:38 +0100 Subject: [PATCH 6/9] add gromacs+cuda --- glicid/packages/chemistry.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/glicid/packages/chemistry.scm b/glicid/packages/chemistry.scm index e7071cb..66c1673 100644 --- a/glicid/packages/chemistry.scm +++ b/glicid/packages/chemistry.scm @@ -28,6 +28,7 @@ (define-public gromacs+cuda (package (inherit gromacs) + (name "gromacs+cuda") (arguments (list #:configure-flags #~(list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests From 0940dfcae0d58056e93f7d30bd32e26e7cabbbad Mon Sep 17 00:00:00 2001 From: Yann Dupont Date: Fri, 3 Feb 2023 18:44:01 +0100 Subject: [PATCH 7/9] =?UTF-8?q?add=20tricks=20for=20suid=20fping=E2=80=A6?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- glicid/packages/monitoring.scm | 32 ++++++++++++++++++++++++++++---- 1 file changed, 28 insertions(+), 4 deletions(-) diff --git a/glicid/packages/monitoring.scm b/glicid/packages/monitoring.scm index 8974d04..82c00d5 100644 --- a/glicid/packages/monitoring.scm +++ b/glicid/packages/monitoring.scm @@ -19,7 +19,15 @@ (version-major+minor version) "/zabbix-" version ".tar.gz")) (sha256 (base32 "0d9aws19rvmsrhkvihnwmr4r1drhl20v9lppdw5wjacp7377xqdy")) -)))) + (modules '((guix build utils))) + (snippet + '(substitute* '("src/zabbix_proxy/proxy.c" + "src/zabbix_server/server.c") + ;; 'fping' must be setuid, so look for it in the usual location. + (("/usr/sbin/fping6?") + "/run/setuid-programs/fping"))))) + +)) (define-public zabbix-agent2 @@ -35,7 +43,15 @@ (version-major+minor version) "/zabbix-" version ".tar.gz")) (sha256 (base32 "0d9aws19rvmsrhkvihnwmr4r1drhl20v9lppdw5wjacp7377xqdy")) -)))) + (modules '((guix build utils))) + (snippet + '(substitute* '("src/zabbix_proxy/proxy.c" + "src/zabbix_server/server.c") + ;; 'fping' must be setuid, so look for it in the usual location. + (("/usr/sbin/fping6?") + "/run/setuid-programs/fping"))))) + +)) (define-public zabbix-server @@ -51,8 +67,16 @@ (version-major+minor version) "/zabbix-" version ".tar.gz")) (sha256 (base32 "0d9aws19rvmsrhkvihnwmr4r1drhl20v9lppdw5wjacp7377xqdy")) + (modules '((guix build utils))) + (snippet + '(substitute* '("src/zabbix_proxy/proxy.c" + "src/zabbix_server/server.c") + ;; 'fping' must be setuid, so look for it in the usual location. + (("/usr/sbin/fping6?") + "/run/setuid-programs/fping"))))) + ) ) -) -) + + From 21c86aace5c34a21dc95c864c3c1a96d84531a06 Mon Sep 17 00:00:00 2001 From: Yann Dupont Date: Fri, 3 Feb 2023 18:59:48 +0100 Subject: [PATCH 8/9] comment out for the moment --- glicid/packages/chemistry.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/glicid/packages/chemistry.scm b/glicid/packages/chemistry.scm index 66c1673..3f7c6bf 100644 --- a/glicid/packages/chemistry.scm +++ b/glicid/packages/chemistry.scm @@ -1,9 +1,8 @@ +#! + (define-module (glicid packages chemistry) #:use-module (guix packages) #:use-module (guix download) - -#:use-module (guix packages) -#:use-module (guix download) #:use-module (guix gexp) #:use-module (guix utils) #:use-module (guix build-system cmake) @@ -23,7 +22,8 @@ #:use-module (gnu packages sphinx) #:use-module (gnu packages check) #:use-module (gnu packages gcc) -#:use-module (non-free cuda)) +#:use-module (non-free cuda) +) (define-public gromacs+cuda (package @@ -78,3 +78,4 @@ (append cuda hwloc)))) ) +!# \ No newline at end of file From 3419da935bbf2658588c4376d6c1916b1f851110 Mon Sep 17 00:00:00 2001 From: Yann Dupont Date: Fri, 3 Feb 2023 19:40:09 +0100 Subject: [PATCH 9/9] now lives in non-free --- glicid/packages/chemistry.scm | 81 ----------------------------------- 1 file changed, 81 deletions(-) delete mode 100644 glicid/packages/chemistry.scm diff --git a/glicid/packages/chemistry.scm b/glicid/packages/chemistry.scm deleted file mode 100644 index 3f7c6bf..0000000 --- a/glicid/packages/chemistry.scm +++ /dev/null @@ -1,81 +0,0 @@ -#! - -(define-module (glicid packages chemistry) - #:use-module (guix packages) - #:use-module (guix download) -#:use-module (guix gexp) -#:use-module (guix utils) -#:use-module (guix build-system cmake) -#:use-module ((guix licenses) #:prefix license:) -#:use-module (gnu packages) -#:use-module (gnu packages algebra) -#:use-module (gnu packages mpi) -#:use-module (gnu packages maths) -#:use-module (gnu packages perl) -#:use-module (gnu packages xml) -#:use-module (gnu packages chemistry) -#:use-module (gnu packages documentation) -#:use-module (gnu packages graphviz) -#:use-module (gnu packages pkg-config) -#:use-module (gnu packages python) -#:use-module (gnu packages python-xyz) -#:use-module (gnu packages sphinx) -#:use-module (gnu packages check) -#:use-module (gnu packages gcc) -#:use-module (non-free cuda) -) - -(define-public gromacs+cuda - (package - (inherit gromacs) - (name "gromacs+cuda") - (arguments - (list #:configure-flags - #~(list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests - ;; Unbundling - "-DGMX_USE_LMFIT=EXTERNAL" - "-DGMX_BUILD_OWN_FFTW=off" - "-DGMX_EXTERNAL_BLAS=on" - "-DGMX_EXTERNAL_LAPACK=on" - "-DGMX_EXTERNAL_TNG=on" - "-DGMX_EXTERNAL_ZLIB=on" - "-DGMX_GPU=CUDA" - (string-append "-DCUDA_TOOLKIT_ROOT_DIR=" #$(this-package-input "cuda-toolkit")) - "-DGMX_EXTERNAL_TINYXML2=on" - (string-append "-DTinyXML2_DIR=" - #$(this-package-input "tinyxml2")) - ;; Workaround for cmake/FindSphinx.cmake version parsing that does - ;; not understand the guix-wrapped `sphinx-build --version' answer - (string-append "-DSPHINX_EXECUTABLE_VERSION=" - #$(package-version python-sphinx))) - #:phases - #~(modify-phases %standard-phases - (add-after 'unpack 'fixes - (lambda* (#:key inputs #:allow-other-keys) - ;; Still bundled: part of gromacs, source behind registration - ;; but free software anyways - ;;(delete-file-recursively "src/external/vmd_molfile") - ;; Still bundled: threads-based OpenMPI-compatible fallback - ;; designed to be bundled like that - ;;(delete-file-recursively "src/external/thread_mpi") - ;; Unbundling - (delete-file-recursively "src/external/lmfit") - (delete-file-recursively "src/external/clFFT") - (delete-file-recursively "src/external/fftpack") - (delete-file-recursively "src/external/build-fftw") - (delete-file-recursively "src/external/tng_io") - (delete-file-recursively "src/external/tinyxml2") - (delete-file-recursively "src/external/googletest") - (copy-recursively #$(package-source googletest) - "src/external/googletest") - ;; This test warns about the build host hardware, disable - (substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp" - (("TEST\\(HardwareTopologyTest, HwlocExecute\\)") - "void __guix_disabled()"))))))) - - (propagated-inputs - (modify-inputs (package-propagated-inputs gromacs) - (append cuda hwloc)))) -) - -!# \ No newline at end of file