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 mode - dependencies |
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45 | ========================== |
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46 | |
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47 | The following software is required, and already available at the ECMWF servers: |
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48 | |
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49 | +---------------------------+-----------------+ |
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50 | | Python code | Fortran code | |
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51 | +---------------------------+-----------------+ |
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52 | | * `Python3`_ | * `gfortran`_ | |
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53 | | * `numpy`_ | * `fftw3`_ | |
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54 | | * `genshi`_ | * `eccodes`_ | |
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55 | | * `eccodes for python`_ | * `emoslib`_ | |
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56 | +---------------------------+-----------------+ |
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57 | |
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58 | |
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59 | .. _ref-prep-remote: |
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60 | |
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61 | Prepare remote environment |
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62 | ========================== |
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63 | |
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64 | ECMWF servers provide all libraries via a module system. Loading the required modules is already built into ``flex_extract`` and no user action is needed. |
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65 | |
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66 | |
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67 | .. _ref-install-remote: |
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68 | |
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69 | Remote installation |
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70 | =================== |
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71 | |
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72 | First, log in on one of the ECMWF servers, such as *ecgate* or *cca/ccb*. |
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73 | Substitute *<ecuid>* with your ECMWF user name: |
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74 | |
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75 | .. code-block:: bash |
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76 | |
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77 | ssh -X <ecuid>@ecaccess.ecmwf.int |
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78 | |
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79 | This will lead to the following output on the command line, asking for your password: |
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80 | |
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81 | .. code-block:: bash |
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82 | |
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83 | Authorized access only. |
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84 | |
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85 | *************************************************************** |
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86 | For further information, read the ECaccess documentation at: |
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87 | |
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88 | https://software.ecmwf.int/wiki/display/ECAC/ECaccess+Home |
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89 | |
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90 | You can also use ECaccess to load & download files from your |
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91 | EChome, ECscratch or ECfs directories using the ECaccess FTP |
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92 | server: |
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93 | |
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94 | ftp://uid@ecaccess.ecmwf.int/ |
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95 | |
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96 | Please note you must use your UID and ActivID code to login! |
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97 | *************************************************************** |
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98 | |
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99 | <ecuid>@<ipname/address>'s password: *** |
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100 | Select hostname (ecgate, cca, ccb) [ecgate]: ecgate |
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101 | |
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102 | [<ecuid>@ecgb11 ~]$ |
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103 | |
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104 | Substitute the *<localuser>* and *<localmachine.tld>* placeholders with your local user name and the IP name or address of your local machine. |
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105 | Untar the file and change into the ``flex_extract`` root directory. |
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106 | |
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107 | .. code-block:: bash |
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108 | |
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109 | scp <localuser>@<localmachine.tld>:</path/to/tarfile/>flex_extract_vX.X.tar.gz $HOME/ |
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110 | cd $HOME |
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111 | tar xvf flex_extract_vX.X.tar.gz |
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112 | cd flex_extract_vX.X |
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113 | |
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114 | |
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115 | |
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116 | Execute the ``setup.sh`` script from the ``flex_extract``'s root directory. |
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117 | Before executing it, it is necessary to adapt some parameters from ``setup.sh`` |
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118 | described in :doc:`../Documentation/Input/setup`. |
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119 | |
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120 | Open ``setup.sh`` with your preferred editor (e.g., nano) and adapt the values: |
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121 | |
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122 | +----------------------------------------------+----------------------------------------------+ |
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123 | | Use this for target = **ectrans** | Use this for target = **cca** or **ccb** | |
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124 | +----------------------------------------------+----------------------------------------------+ |
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125 | | .. code-block:: bash | .. code-block:: bash | |
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126 | | | | |
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127 | | ... | ... | |
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128 | | # -----------------------------------------| # -----------------------------------------| |
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129 | | # AVAILABLE COMMANDLINE ARGUMENTS TO SET | # AVAILABLE COMMANDLINE ARGUMENTS TO SET | |
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130 | | # | # | |
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131 | | # THE USER HAS TO SPECIFY THESE PARAMETER | # THE USER HAS TO SPECIFY THESE PARAMETER | |
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132 | | # | # | |
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133 | | TARGET='ecgate' | TARGET='cca' | |
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134 | | MAKEFILE='makefile_ecgate' | MAKEFILE='makefile_cray' | |
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135 | | ECUID='<username>' | ECUID='<username>' | |
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136 | | ECGID='<groupID>' | ECGID='<groupID>' | |
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137 | | GATEWAY='<gatewayname>' | GATEWAY='<gatewayname>' | |
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138 | | DESTINATION='<username>@genericSftp' | DESTINATION='<username>@genericSftp' | |
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139 | | INSTALLDIR=None | INSTALLDIR='' | |
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140 | | JOB_TEMPLATE='job.template' | JOB_TEMPLATE='job.template' | |
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141 | | CONTROLFILE='CONTROL_EA5' | CONTROLFILE='CONTROL_EA5' | |
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142 | | ... | ... | |
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143 | +----------------------------------------------+----------------------------------------------+ |
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144 | |
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145 | :underline:`Please substitute the values of ECUID and ECGID |
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146 | with your own ones (look at any of your files with ``ls -l'' to see uid and gid).` |
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147 | |
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148 | .. note:: |
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149 | |
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150 | If a local gateway server is available, files can be transferred with ``ECaccess`` commands. In that case, a valid *GATEWAY* and *DESTINATION* have to be present in the ``setup.sh`` file (even if not used, the lines must not be deleted). |
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151 | |
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152 | Afterwards, type: |
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153 | |
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154 | .. code-block:: bash |
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155 | |
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156 | module load python3 |
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157 | ./setup.sh |
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158 | |
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159 | to start the installation. You should see the following on standard output. |
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160 | |
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161 | |
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162 | .. code-block:: bash |
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163 | |
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164 | # Output of setup.sh |
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165 | Create tarball ... |
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166 | Job compilation script has been submitted to ecgate for installation in ${HOME}/flex_extract_vX.X |
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167 | You should get an email with subject "flexcompile" within the next few minutes! |
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168 | |
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169 | |
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170 | ``Flex_extract`` automatically uses the email address connected to the user account on ECMWF servers. The email content should look like this with a "SUCCESS" statement in the last line: |
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171 | |
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172 | .. code-block:: bash |
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173 | |
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174 | gfortran -O3 -march=native -L/usr/local/apps/eccodes/2.13.0/GNU/7.3.0/lib -Wl,-rpath,/usr/local/apps/eccodes/2.13.0/GNU/7.3.0/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 -I. -I/usr/local/apps/eccodes/2.13.0/GNU/7.3.0/include -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./rwgrib2.f90 |
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175 | gfortran -O3 -march=native -L/usr/local/apps/eccodes/2.13.0/GNU/7.3.0/lib -Wl,-rpath,/usr/local/apps/eccodes/2.13.0/GNU/7.3.0/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 -I. -I/usr/local/apps/eccodes/2.13.0/GNU/7.3.0/include -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./phgrreal.f90 |
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176 | gfortran -O3 -march=native -L/usr/local/apps/eccodes/2.13.0/GNU/7.3.0/lib -Wl,-rpath,/usr/local/apps/eccodes/2.13.0/GNU/7.3.0/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 -I. -I/usr/local/apps/eccodes/2.13.0/GNU/7.3.0/include -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./grphreal.f90 |
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177 | gfortran -O3 -march=native -L/usr/local/apps/eccodes/2.13.0/GNU/7.3.0/lib -Wl,-rpath,/usr/local/apps/eccodes/2.13.0/GNU/7.3.0/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 -I. -I/usr/local/apps/eccodes/2.13.0/GNU/7.3.0/include -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./ftrafo.f90 |
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178 | gfortran -O3 -march=native -L/usr/local/apps/eccodes/2.13.0/GNU/7.3.0/lib -Wl,-rpath,/usr/local/apps/eccodes/2.13.0/GNU/7.3.0/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 -I. -I/usr/local/apps/eccodes/2.13.0/GNU/7.3.0/include -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./calc_etadot.f90 |
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179 | gfortran -O3 -march=native -L/usr/local/apps/eccodes/2.13.0/GNU/7.3.0/lib -Wl,-rpath,/usr/local/apps/eccodes/2.13.0/GNU/7.3.0/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 -I. -I/usr/local/apps/eccodes/2.13.0/GNU/7.3.0/include -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./posnam.f90 |
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180 | gfortran rwgrib2.o calc_etadot.o ftrafo.o grphreal.o posnam.o phgrreal.o -o calc_etadot_fast.out -O3 -march=native -L/usr/local/apps/eccodes/2.13.0/GNU/7.3.0/lib -Wl,-rpath,/usr/local/apps/eccodes/2.13.0/GNU/7.3.0/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 -fopenmp |
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181 | ln -sf calc_etadot_fast.out calc_etadot |
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182 | lrwxrwxrwx. 1 <username> at 20 Mar 8 14:11 calc_etadot -> calc_etadot_fast.out |
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183 | SUCCESS! |
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184 | |
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