[30f7911] | 1 | ************************ |
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| 2 | Remote mode installation |
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| 3 | ************************ |
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| 4 | |
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| 5 | .. role:: underline |
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| 6 | :class: underline |
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| 7 | |
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| 8 | .. toctree:: |
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| 9 | :hidden: |
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| 10 | :maxdepth: 2 |
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| 11 | |
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| 12 | |
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| 13 | .. _Python 3: https://docs.python.org/3/ |
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| 14 | .. _Python3: https://www.python.org/downloads/ |
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| 15 | .. _Anaconda Python3: https://www.anaconda.com/distribution/#download-section |
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| 16 | |
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| 17 | .. _numpy: http://www.numpy.org/ |
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| 18 | .. _ecmwf-api-client: https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home |
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| 19 | .. _cdsapi: https://cds.climate.copernicus.eu/api-how-to |
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| 20 | .. _genshi: https://genshi.edgewall.org/ |
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| 21 | .. _eccodes for python: https://packages.debian.org/sid/python3-eccodes |
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| 22 | .. _eccodes for conda: https://anaconda.org/conda-forge/eccodes |
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| 23 | .. _gfortran: https://gcc.gnu.org/wiki/GFortran |
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| 24 | .. _fftw3: http://www.fftw.org |
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| 25 | .. _eccodes: https://software.ecmwf.int/wiki/display/ECC |
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| 26 | .. _emoslib: https://software.ecmwf.int/wiki/display/EMOS/Emoslib |
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| 27 | .. _member state: https://www.ecmwf.int/en/about/who-we-are/member-states |
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| 28 | .. _registration form: https://apps.ecmwf.int/registration/ |
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| 29 | .. _CDS API registration: https://cds.climate.copernicus.eu/user/register |
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| 30 | .. _ECMWF ectrans site: https://confluence.ecmwf.int/display/ECAC/Unattended+file+transfer+-+ectrans |
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| 31 | .. _ECaccess Presentation: https://confluence.ecmwf.int/download/attachments/45759146/ECaccess.pdf |
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| 32 | .. _ECMWF's instructions on gateway server: https://confluence.ecmwf.int/display/ECAC/ECaccess+Home |
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| 33 | .. _Computing Representative: https://www.ecmwf.int/en/about/contact-us/computing-representatives |
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| 34 | .. _MARS access: https://confluence.ecmwf.int//display/WEBAPI/Access+MARS |
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| 35 | |
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| 36 | .. _download section: https://www.flexpart.eu/downloads |
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| 37 | |
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| 38 | |
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| 39 | .. _ref-remote-mode: |
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| 40 | |
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| 41 | |
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| 42 | .. _ref-req-remote: |
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| 43 | |
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| 44 | Remote environment requirements |
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| 45 | =============================== |
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| 46 | |
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| 47 | The environment for ``flex_extract`` on ECMWF servers has to provide these |
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| 48 | software packages and libraries: |
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| 49 | |
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| 50 | +---------------------------+-----------------+ |
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| 51 | | Python part | Fortran part | |
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| 52 | +---------------------------+-----------------+ |
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| 53 | | * `Python3`_ | * `gfortran`_ | |
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| 54 | | * `numpy`_ | * `fftw3`_ | |
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| 55 | | * `genshi`_ | * `eccodes`_ | |
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| 56 | | * `eccodes for python`_ | * `emoslib`_ | |
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| 57 | +---------------------------+-----------------+ |
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| 58 | |
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| 59 | |
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| 60 | .. _ref-prep-remote: |
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| 61 | |
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| 62 | Prepare remote environment |
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| 63 | ========================== |
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| 64 | |
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| 65 | The environment on the ECMWF server (such as *ecgate* or *cca*) is already |
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| 66 | prepared. ECMWF server provide all libraries via a module system which is |
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| 67 | going to be selected by ``flex_extract`` automatically. |
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| 68 | |
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| 69 | |
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| 70 | .. _ref-install-remote: |
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| 71 | |
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| 72 | Remote installation |
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| 73 | =================== |
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| 74 | |
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| 75 | First, log in on one of the ECMWF Linux server, such as *ecgate* or *cca/ccb*. |
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| 76 | Substitute *<ecuid>* with your ECMWF user name: |
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| 77 | |
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| 78 | .. code-block:: bash |
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| 79 | |
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| 80 | ssh -X <ecuid>@ecaccess.ecmwf.int |
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| 81 | |
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| 82 | This will lead to the following output on the command line, asking for your |
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| 83 | password: |
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| 84 | |
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| 85 | .. code-block:: bash |
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| 86 | |
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| 87 | Authorized access only. |
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| 88 | |
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| 89 | *************************************************************** |
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| 90 | For further information, read the ECaccess documentation at: |
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| 91 | |
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| 92 | https://software.ecmwf.int/wiki/display/ECAC/ECaccess+Home |
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| 93 | |
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| 94 | You can also use ECaccess to load & download files from your |
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| 95 | EChome, ECscratch or ECfs directories using the ECaccess FTP |
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| 96 | server: |
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| 97 | |
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| 98 | ftp://uid@ecaccess.ecmwf.int/ |
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| 99 | |
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| 100 | Please note you must use your UID and ActivID code to login! |
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| 101 | *************************************************************** |
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| 102 | |
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| 103 | <ecuid>@131.130.157.5's password: *** |
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| 104 | Select hostname (ecgate, cca, ccb) [ecgate]: ecgate |
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| 105 | |
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| 106 | [<ecuid>@ecgb11 ~]$ |
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| 107 | |
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| 108 | |
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| 109 | Then, copy the ``flex_extract`` tar ball (from section :ref:`ref-download`) |
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| 110 | to the ``$HOME`` directory of the ECMWF Linux server via ``scp``. |
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| 111 | Substitute the *<localuser>* and *<server.edu>* placeholders with your credentials. |
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| 112 | Untar the file and change into the ``flex_extract`` root directory. |
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| 113 | |
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| 114 | .. code-block:: bash |
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| 115 | |
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| 116 | scp <localuser>@<server.edu>:/path/to/tarfile/flex_extract_vX.X.tar.gz $HOME/ |
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| 117 | cd $HOME |
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| 118 | tar xvf flex_extract_vX.X.tar.gz |
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| 119 | cd flex_extract_vX.X |
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| 120 | |
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| 121 | |
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| 122 | On these ECMWF servers, it is not necessary to prepare the environment or the |
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| 123 | ``Makefile`` for the Fortran program (``CONVERT2``) as described above. |
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| 124 | All third party libraries are available from a module system. The ``Makefile`` |
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| 125 | is optimized for ECMWF servers and the compilation |
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| 126 | script ``compilejob.ksh``, which will be submitted by ``flex_extract`` to the |
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| 127 | batch job queue at ECMWF, does load all relevant modules from the ECMWF's module system. |
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| 128 | |
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| 129 | So there is just the need to execute the ``setup.sh`` script from the |
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| 130 | ``flex_extract`` root directory for installation. |
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| 131 | Before executing it, it is necessary to adapt some parameters from ``setup.sh`` |
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| 132 | described in :doc:`Documentation/Input/setup`. |
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| 133 | |
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| 134 | Open ``setup.sh`` with your editor and adapt the values: |
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| 135 | |
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| 136 | +----------------------------------------------+----------------------------------------------+ |
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| 137 | | Take this for target = **ectrans** | Take this for target = **cca** | |
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| 138 | +----------------------------------------------+----------------------------------------------+ |
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| 139 | | .. code-block:: bash | .. code-block:: bash | |
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| 140 | | | | |
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| 141 | | ... | ... | |
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| 142 | | # -----------------------------------------| # -----------------------------------------| |
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| 143 | | # AVAILABLE COMMANDLINE ARGUMENTS TO SET | # AVAILABLE COMMANDLINE ARGUMENTS TO SET | |
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| 144 | | # | # | |
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| 145 | | # THE USER HAS TO SPECIFY THESE PARAMETER | # THE USER HAS TO SPECIFY THESE PARAMETER | |
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| 146 | | # | # | |
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| 147 | | TARGET='ecgate' | TARGET='cca' | |
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| 148 | | MAKEFILE='Makefile.gfortran' | MAKEFILE='Makefile.CRAY' | |
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| 149 | | ECUID='uid' | ECUID='uid' | |
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| 150 | | ECGID='gid' | ECGID='gid' | |
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| 151 | | GATEWAY=None | GATEWAY=None | |
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| 152 | | DESTINATION=None | DESTINATION=None | |
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| 153 | | INSTALLDIR=None | INSTALLDIR='' | |
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| 154 | | JOB_TEMPLATE='job.template' | JOB_TEMPLATE='job.template' | |
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| 155 | | CONTROLFILE='CONTROL_EA5' | CONTROLFILE='CONTROL_EA5' | |
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| 156 | | ... | ... | |
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| 157 | +----------------------------------------------+----------------------------------------------+ |
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| 158 | |
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| 159 | :underline:`Please substitute the values of ECUID and ECGID |
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| 160 | with your own credentials and settings.` |
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| 161 | |
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| 162 | .. note:: |
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| 163 | |
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| 164 | If a local gateway server is available the transfer of files could be done |
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| 165 | via the ``ECaccess`` commands. Therefore a valid *GATEWAY* and *DESTINATION* |
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| 166 | have to be present and should be set in the ``setup.sh`` file. |
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| 167 | |
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| 168 | |
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| 169 | Afterwards, type: |
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| 170 | |
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| 171 | .. code-block:: bash |
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| 172 | |
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| 173 | module load python3 |
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| 174 | ./setup.sh |
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| 175 | |
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| 176 | to start the installation. You should see the following output at the command line. |
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| 177 | |
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| 178 | |
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| 179 | .. code-block:: bash |
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| 180 | |
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| 181 | # Output of setup.sh |
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| 182 | Create tarball ... |
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| 183 | Job compilation script has been submitted to ecgate for installation in ${HOME}/flex_extract_vX.X |
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| 184 | You should get an email with subject "flexcompile" within the next few minutes! |
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| 185 | |
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| 186 | |
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| 187 | The email content should look like this with a "SUCCESS" statement in the last line: |
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| 188 | |
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| 189 | .. code-block:: bash |
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| 190 | |
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| 191 | gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp phgrreal.f |
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| 192 | gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp grphreal.f |
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| 193 | gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp ftrafo.f |
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| 194 | gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g rwGRIB2.f90 |
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| 195 | gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g posnam.f |
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| 196 | gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g preconvert.f90 |
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| 197 | gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -g -O3 -o ./CONVERT2 ftrafo.o phgrreal.o grphreal.o rwGRIB2.o posnam.o preconvert.o -L/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -leccodes_f90 -leccodes -ljasper -lpthread -L/usr/local/apps/jasper/1.900.1/LP64/lib -ljasper -lm -L/usr/local/apps/libemos/000455/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/libemos/000455/GNU/6.3.0/lib -lemos.R64.D64.I32 -L/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -lfftw3 |
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| 198 | -rwxr-x---. 1 USER at 353134 May 23 12:27 CONVERT2 |
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| 199 | SUCCESS! |
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| 200 | |
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| 201 | |
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| 204 | |
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