From 1120d572fa82034cedbf193c0b7d0cc8c3fc954a Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 9 Jul 2019 17:18:05 +0200 Subject: [PATCH 01/10] Cleaning allocation of string --- src/utils/c_functions.f90 | 4 +++- src/zmq/utils.irp.f | 10 ++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/src/utils/c_functions.f90 b/src/utils/c_functions.f90 index 32bd5005..52c01d12 100644 --- a/src/utils/c_functions.f90 +++ b/src/utils/c_functions.f90 @@ -15,5 +15,7 @@ subroutine usleep(us) use iso_c_binding implicit none integer, intent(in) :: us - call usleep_c(int(us,c_int)) + integer(c_int) :: u + u = us + call usleep_c(u) end diff --git a/src/zmq/utils.irp.f b/src/zmq/utils.irp.f index e936f268..e76238ed 100644 --- a/src/zmq/utils.irp.f +++ b/src/zmq/utils.irp.f @@ -300,7 +300,6 @@ function new_zmq_push_socket(thread) END_DOC integer, intent(in) :: thread integer :: rc - character*(8), external :: zmq_port integer(ZMQ_PTR) :: new_zmq_push_socket call omp_set_lock(zmq_lock) @@ -424,7 +423,6 @@ subroutine end_zmq_pair_socket(zmq_socket_pair) END_DOC integer(ZMQ_PTR), intent(in) :: zmq_socket_pair integer :: rc - character*(8), external :: zmq_port call omp_set_lock(zmq_lock) rc = f77_zmq_close(zmq_socket_pair) @@ -444,7 +442,6 @@ subroutine end_zmq_pull_socket(zmq_socket_pull) END_DOC integer(ZMQ_PTR), intent(in) :: zmq_socket_pull integer :: rc - character*(8), external :: zmq_port ! rc = f77_zmq_setsockopt(zmq_socket_pull,ZMQ_LINGER,0,4) ! if (rc /= 0) then @@ -471,7 +468,6 @@ subroutine end_zmq_push_socket(zmq_socket_push,thread) integer, intent(in) :: thread integer(ZMQ_PTR), intent(in) :: zmq_socket_push integer :: rc - character*(8), external :: zmq_port rc = f77_zmq_setsockopt(zmq_socket_push,ZMQ_LINGER,300000,4) if (rc /= 0) then @@ -751,10 +747,12 @@ integer function add_task_to_taskserver(zmq_to_qp_run_socket,task) character*(*), intent(in) :: task integer :: rc, sze - character(len=:), allocatable :: message + character(len=:), allocatable :: message add_task_to_taskserver = 0 + sze = len(trim(task)) + len(trim(zmq_state))+11 + allocate(character(len=sze) :: message) message='add_task '//trim(zmq_state)//' '//trim(task) sze = len(message) rc = f77_zmq_send(zmq_to_qp_run_socket, message, sze, 0) @@ -770,6 +768,7 @@ integer function add_task_to_taskserver(zmq_to_qp_run_socket,task) add_task_to_taskserver = -1 return endif + deallocate(message) end @@ -1031,7 +1030,6 @@ subroutine end_zmq_to_qp_run_socket(zmq_to_qp_run_socket) ! Terminate the socket from the application to qp_run END_DOC integer(ZMQ_PTR), intent(in) :: zmq_to_qp_run_socket - character*(8), external :: zmq_port integer :: rc rc = f77_zmq_setsockopt(zmq_to_qp_run_socket,ZMQ_LINGER,300000,4) From edd2276b75fb24a54e36ff86bce8f72a0ba98597 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 9 Jul 2019 17:33:44 +0200 Subject: [PATCH 02/10] Fixed usleep --- src/utils/c_funcs.c | 6 ++++++ src/utils/c_functions.f90 | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) create mode 100644 src/utils/c_funcs.c diff --git a/src/utils/c_funcs.c b/src/utils/c_funcs.c new file mode 100644 index 00000000..5b7035fb --- /dev/null +++ b/src/utils/c_funcs.c @@ -0,0 +1,6 @@ +#include + +void usleep_c(int s) +{ + usleep((useconds_t) s); +} diff --git a/src/utils/c_functions.f90 b/src/utils/c_functions.f90 index 52c01d12..425aafd6 100644 --- a/src/utils/c_functions.f90 +++ b/src/utils/c_functions.f90 @@ -2,7 +2,7 @@ module c_functions use iso_c_binding interface - subroutine usleep_c(us) bind (C,name="usleep") + subroutine usleep_c(us) bind (C,name="usleep_c") use iso_c_binding integer(c_int), value :: us end subroutine usleep_c From a8dbea61d3d542089fb61c7392b5060508735d33 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Wed, 24 Jul 2019 08:11:17 +0200 Subject: [PATCH 03/10] Fixed opam installation --- INSTALL.rst | 11 +++++++++-- configure | 6 ++++-- 2 files changed, 13 insertions(+), 4 deletions(-) diff --git a/INSTALL.rst b/INSTALL.rst index c91b184f..10f583db 100644 --- a/INSTALL.rst +++ b/INSTALL.rst @@ -328,7 +328,7 @@ OCaml echo ${QP_ROOT}/bin ${QP_ROOT}/external/opam_installer.sh --no-backup --fresh - You the :command:`opam` command can be installed in the :file:`${QP_ROOT}/bin` + The :command:`opam` command can be installed in the :file:`${QP_ROOT}/bin` directory. To do this, take the output of ``echo ${QP_ROOT}/bin`` and use it as an answer to where :command:`opam` should be installed. @@ -337,7 +337,14 @@ OCaml .. code:: bash - opam init --disable-sandboxing --comp=4.07.0 + opam init --comp=4.07.1 + eval `${QP_ROOT}/bin/opam env` + + If the installation fails because of bwrap, the you can initialize opam using: + + .. code:: bash + + opam init --disable-sandboxing --comp=4.07.1 eval `${QP_ROOT}/bin/opam env` * Install the required external OCaml libraries diff --git a/configure b/configure index c343c243..c3ff8942 100755 --- a/configure +++ b/configure @@ -297,12 +297,13 @@ EOF ${QP_ROOT}/bin + EOF rm ${QP_ROOT}/external/opam_installer.sh source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true - ${QP_ROOT}/bin/opam init --verbose --yes + ${QP_ROOT}/bin/opam init --verbose --yes --comp=4.07.1 --disable-sandboxing eval $(${QP_ROOT}/bin/opam env) opam install -y ${OCAML_PACKAGES} || exit 1 @@ -310,13 +311,14 @@ EOF # Conventional commands execute << EOF chmod +x "\${QP_ROOT}"/external/opam_installer.sh + "\${QP_ROOT}"/external/opam_installer.sh --no-backup rm --force \${QP_ROOT}/bin/opam export OPAMROOT=\${OPAMROOT:-\${QP_ROOT}/external/opam} echo \${QP_ROOT}/bin \ | sh \${QP_ROOT}/external/opam_installer.sh rm \${QP_ROOT}/external/opam_installer.sh source \${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true - \${QP_ROOT}/bin/opam init --verbose --yes + \${QP_ROOT}/bin/opam init --verbose --yes --comp=4.07.1 --disable-sandboxing eval \$(\${QP_ROOT}/bin/opam env) opam install -y \${OCAML_PACKAGES} || exit 1 EOF From 4e58fe7576b320c6c282762f3df538397f413aeb Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Wed, 24 Jul 2019 08:12:22 +0200 Subject: [PATCH 04/10] Typo --- INSTALL.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/INSTALL.rst b/INSTALL.rst index 10f583db..a9cee40b 100644 --- a/INSTALL.rst +++ b/INSTALL.rst @@ -340,7 +340,7 @@ OCaml opam init --comp=4.07.1 eval `${QP_ROOT}/bin/opam env` - If the installation fails because of bwrap, the you can initialize opam using: + If the installation fails because of bwrap, you can initialize opam using: .. code:: bash From c405dc99d3cdd1c9ffa6afc6bb8f91758a1321e5 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Wed, 24 Jul 2019 09:06:11 +0200 Subject: [PATCH 05/10] Fixing travis --- configure | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/configure b/configure index c3ff8942..634b5888 100755 --- a/configure +++ b/configure @@ -303,22 +303,30 @@ EOF rm ${QP_ROOT}/external/opam_installer.sh source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true - ${QP_ROOT}/bin/opam init --verbose --yes --comp=4.07.1 --disable-sandboxing + execute << EOF + ${QP_ROOT}/bin/opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing eval $(${QP_ROOT}/bin/opam env) opam install -y ${OCAML_PACKAGES} || exit 1 +EOF else # Conventional commands execute << EOF chmod +x "\${QP_ROOT}"/external/opam_installer.sh "\${QP_ROOT}"/external/opam_installer.sh --no-backup +EOF + execute << EOF rm --force \${QP_ROOT}/bin/opam export OPAMROOT=\${OPAMROOT:-\${QP_ROOT}/external/opam} echo \${QP_ROOT}/bin \ | sh \${QP_ROOT}/external/opam_installer.sh +EOF + execute << EOF rm \${QP_ROOT}/external/opam_installer.sh source \${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true - \${QP_ROOT}/bin/opam init --verbose --yes --comp=4.07.1 --disable-sandboxing + \${QP_ROOT}/bin/opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing +EOF + execute << EOF eval \$(\${QP_ROOT}/bin/opam env) opam install -y \${OCAML_PACKAGES} || exit 1 EOF From be6c9b533ead2710e12e69107a3edb705d2e6180 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Wed, 24 Jul 2019 09:36:51 +0200 Subject: [PATCH 06/10] Fixing travis --- configure | 2 ++ 1 file changed, 2 insertions(+) diff --git a/configure b/configure index 634b5888..228b4f3f 100755 --- a/configure +++ b/configure @@ -304,6 +304,7 @@ EOF source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true execute << EOF + opam switch 4.07.1 || exit 1 ${QP_ROOT}/bin/opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing eval $(${QP_ROOT}/bin/opam env) @@ -324,6 +325,7 @@ EOF execute << EOF rm \${QP_ROOT}/external/opam_installer.sh source \${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true + opam switch 4.07.1 || exit 1 \${QP_ROOT}/bin/opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing EOF execute << EOF From 00074558463e79e00bf130f4ae437d8a161d094c Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Wed, 24 Jul 2019 10:27:39 +0200 Subject: [PATCH 07/10] Fixing travis --- configure | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/configure b/configure index 228b4f3f..e605c088 100755 --- a/configure +++ b/configure @@ -304,7 +304,7 @@ EOF source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true execute << EOF - opam switch 4.07.1 || exit 1 + opam switch create ocaml-base-compiler.4.07.1 || exit 1 ${QP_ROOT}/bin/opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing eval $(${QP_ROOT}/bin/opam env) @@ -325,7 +325,7 @@ EOF execute << EOF rm \${QP_ROOT}/external/opam_installer.sh source \${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true - opam switch 4.07.1 || exit 1 + opam switch create ocaml-base-compiler.4.07.1 || exit 1 \${QP_ROOT}/bin/opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing EOF execute << EOF From 2f89be4ee9ec6c29d167b4b1021d33d90c5160c2 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Wed, 24 Jul 2019 12:33:08 +0200 Subject: [PATCH 08/10] Fixing travis --- configure | 20 +++++++++----------- 1 file changed, 9 insertions(+), 11 deletions(-) diff --git a/configure b/configure index e605c088..98641633 100755 --- a/configure +++ b/configure @@ -303,13 +303,12 @@ EOF rm ${QP_ROOT}/external/opam_installer.sh source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true - execute << EOF - opam switch create ocaml-base-compiler.4.07.1 || exit 1 - ${QP_ROOT}/bin/opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing + opam switch create ocaml-base-compiler.4.07.1 + opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing - eval $(${QP_ROOT}/bin/opam env) + eval $(opam env) opam install -y ${OCAML_PACKAGES} || exit 1 -EOF + else # Conventional commands execute << EOF @@ -322,14 +321,13 @@ EOF echo \${QP_ROOT}/bin \ | sh \${QP_ROOT}/external/opam_installer.sh EOF - execute << EOF - rm \${QP_ROOT}/external/opam_installer.sh - source \${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true - opam switch create ocaml-base-compiler.4.07.1 || exit 1 - \${QP_ROOT}/bin/opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing + rm \${QP_ROOT}/external/opam_installer.sh + source \${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true + opam switch create ocaml-base-compiler.4.07.1 || exit 1 + opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing + eval $(opam env) EOF execute << EOF - eval \$(\${QP_ROOT}/bin/opam env) opam install -y \${OCAML_PACKAGES} || exit 1 EOF fi From 861aed9dd4c0a9c8fe2183a9892f68ec2f64b03c Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Wed, 24 Jul 2019 12:40:05 +0200 Subject: [PATCH 09/10] Update GITHUB.md --- GITHUB.md | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/GITHUB.md b/GITHUB.md index 02836a37..cee4cc8c 100644 --- a/GITHUB.md +++ b/GITHUB.md @@ -2,20 +2,23 @@ GitHub Branches =============== master: - The current up-to-date working branch, that users download It should - only contain the latest release and bug fixes. + The current up-to-date working branch, that users download. It should + only contain the latest stable release and bug fixes. -develop-lcpq: - Toulouse development branch - -develop-lct: - Paris development branch - -develop: +dev: It is a fork of the *master* branch with new developments that will be merged in the *master* branch for the next release. Other development branches should be merged on this one. +bugfix: + A fork of the *master* on which the bug fixes are made. + +dev-lcpq: + Toulouse development branch + +dev-lct: + Paris development branch + gh-pages: This is an independent branch, containing only the web site of QP2. From 2e86462070aff808cb15b50f6613a84f99cf7c55 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Wed, 24 Jul 2019 12:56:45 +0200 Subject: [PATCH 10/10] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e7fab0c9..3349f561 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ [*Quantum package 2.0: an open-source determinant-driven suite of programs*](https://pubs.acs.org/doi/10.1021/acs.jctc.9b00176)\ Y. Garniron, K. Gasperich, T. Applencourt, A. Benali, A. Ferté, J. Paquier, B. Pradines, R. Assaraf, P. Reinhardt, J. Toulouse, P. Barbaresco, N. Renon, G. David, J. P. Malrieu, M. Véril, M. Caffarel, P. F. Loos, E. Giner and A. Scemama\ -J. Chem. Theory Comput., 15:6, 3591--3609, (2019)\ +[J. Chem. Theory Comput. 2019, 15, 6, 3591-3609](https://doi.org/10.1021/acs.jctc.9b00176)\ https://arxiv.org/abs/1902.08154 ```