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59 60 61<style> 62@media (min-width: 1201px) { 63 .header .nav li { 64 margin-right: 49px; 65 margin-bottom: 0; 66 } 67} 68</style> 69 70 71 </head> 72 73 <body> 74 <header class="header" id="header"> 75 <div class="container-xxl container d-flex align-items-center position-xl-relative justify-content-center px-xxl-0"> 76 <div class="callnav d-xl-none" id="navCall"> 77 <span class="icon"><img src="/images/nav-menu-icon.svg" height="34" width="34" alt="" /></span> 78 </div> 79 <div class="brand"> 80 <a href="/"><img src="/images/logo_new.jpg" alt="" height="100" width="255" /></a> 81 </div> 82 <nav class="navsite d-none d-xl-flex ms-auto align-items-center" id="navSite" aria-label="Navigation"> 83 <ul class="nav"> 84 <li class=""><a href="/">Home</a></li> 85 <li class="active"><a href="/faqs">FAQs</a></li> 86 <li class=""><a href="/support">Support</a></li> 87 <li class=""><a href="/status">Status</a></li> 88 <li class=""><a href="/blogs">This Week</a></li> 89 <li class=""><a href="/about">About</a></li> 90<!-- <li class=""><a href="/pricing">Free Account</a></li>--> 91 92 <li class="logged_in "><a href="/portal2/login!input.action">Log in</a></li> 93 94 </ul> 95 </nav> 96 97<!-- <div class="cta-nav d-none d-md-block logged_in"><a class="cta" href="/portal2/register.action">Free Trial!</a></div>--> 98 </div> 99 </header> 100 101 102 103 <section class="hero inner"> 104 <div class="img-hero"><img class="w-100 " src="images/faqs-hero.png" alt="" /></div> 105 <div class="hero-text"> 106 <h1 class="mb-0 mb-0">Frequently Asked Questions</h1> 107 </div> 108 </section> 109 <section class="sec punch" style="background-image: url(images/bg-bond.jpg)"> 110 <div class="container-xxl container text-center"> 111 112 <p>We welcome your questions, comments and bug reports. If you don't find the answer below, try the <a href="/support">Support page</a> or search our <a href="#">Google Group</a>. If you still can't find the answer, contact us through our Google group. We generally respond within 24 hours.</p> 113 114 <!-- <p>We are always available to answer your questions. If you don't find the answer below, try the <a href="support.html">Support page</a> or search our <a href="#">Google Group</a>. If you still can't find the answer, just ask us there. We're online!</p> --> 115 116 </div> 117 </section> 118 <section class="sec fold"> 119 <div class="container-xxl container"> 120 121 <div class="item"> 122 <div class="head d-flex justify-content-between align-items-center"> 123 <h2 class="mb-0 flex-grow-1">My registration failed, Help!</h2> 124 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 125 </div> 126 <div class="block"> 127 <div class="fold-content"> 128 <p><strong>There are two ways a registration might fail:</strong></p> 129 130<p>1. You registered successfully, but did not receive an activation email. Globally servers are very concerned about SPAM and pfishing, so our activation email occasionally does not make it to the user. If you don't see the email in your personal SPAM catcher, it is best to just contact us, and we will activate on our side.</p> 131 132<p>2. You tried to register, but received a warning that your registration could not be completed. This may happen because CIPRES does not allow a user to hold multiple accounts. The application automatically prevents registration of a second account by a single user. If you see this message, just contact us through the email referenced in the message. We can help.</p> 133 <!-- <p>There are two ways a registration might fail:</p> 134 <ol> 135 <li>You registered successfully, but did not receive an activation email. Globally servers are very concerned about SPAM and pfishing, so our activation email occasionally does not make it to the user. If you don't see the email in your personal SPAM catcher, it is best to just contact us, and we will activate on our side.</li> 136 <li>You tried to register, but received a warning that your registration could not be completed. This may happen because CIPRES does not allow a user to hold multiple accounts. The application automatically prevents registration of a second account by a single user. If you see this message, just contact us through the email referenced in the message. We can help.</li> 137 </ol> --> 138 </div> 139 </div>
140 </div> 141 142 <div class="item"> 143 <div class="head d-flex justify-content-between align-items-center"> 144 <h2 class="mb-0 flex-grow-1">Where can I learn how to use CIPRES?</h2> 145 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 146 </div> 147 <div class="block"> 148 <div class="fold-content"> 149 <p><strong>Basic CIPRES Science Gateway Usage</strong>:<br /> 150The CIPRES Science Gateway interface manages data in folders, much like an e-mail client. The data is then used to stage individual jobs (also stroed in folders). Here we provide some flash demos to illustrate the basic functionalities of the CIPRES Science Gateway. Each demo is less than 3 minutes.</p> 151 152<ul> 153 <li><a href="http://www.phylo.org/tools/flash/cipresportal2_data_management.htm">How to manage data and folders in the CIPRES Science Gateway</a></li> 154 <li><a href="http://www.phylo.org/tools/flash/cipresportal2_task_management.htm">How to run jobs in the CIPRES Science Gateway</a></li> 155</ul> 156 157<p><strong>Known General Issues</strong>: <a href="https://www.phylo.org/index.php/help/issues2">here</a>.</p> 158 159<p><strong>Code Specific Issues</strong>: <a href="https://www.phylo.org/index.php/help/issues">here.</a></p> 160 161<p><strong>Supported Formats:</strong> <a href="https://www.phylo.org/index.php/help/requirements">here.</a></p> 162 <!-- <p>There are two ways a registration might fail:</p> 163 <ol> 164 <li>You registered successfully, but did not receive an activation email. Globally servers are very concerned about SPAM and pfishing, so our activation email occasionally does not make it to the user. If you don't see the email in your personal SPAM catcher, it is best to just contact us, and we will activate on our side.</li> 165 <li>You tried to register, but received a warning that your registration could not be completed. This may happen because CIPRES does not allow a user to hold multiple accounts. The application automatically prevents registration of a second account by a single user. If you see this message, just contact us through the email referenced in the message. We can help.</li> 166 </ol> --> 167 </div> 168 </div> 169 </div> 170 171 <div class="item"> 172 <div class="head d-flex justify-content-between align-items-center"> 173 <h2 class="mb-0 flex-grow-1">Can you handle GB input files?</h2> 174 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 175 </div> 176 <div class="block"> 177 <div class="fold-content"> 178 <p>CIPRES offers a Globus file transfer tool that allows you to upload files that are in the GB range without using http protocols.<br /> 179Globus uploads are fast (if your internet has a decent upload speed) and robust/resumable. CIPRES can handle individual files up to 16 GB. You can find more information about Globus transfers on our <a href="http://www.phylo.org/index.php/help/videos">video support page.</a></p> 180 <!-- <p>There are two ways a registration might fail:</p> 181 <ol> 182 <li>You registered successfully, but did not receive an activation email. Globally servers are very concerned about SPAM and pfishing, so our activation email occasionally does not make it to the user. If you don't see the email in your personal SPAM catcher, it is best to just contact us, and we will activate on our side.</li> 183 <li>You tried to register, but received a warning that your registration could not be completed. This may happen because CIPRES does not allow a user to hold multiple accounts. The application automatically prevents registration of a second account by a single user. If you see this message, just contact us through the email referenced in the message. We can help.</li> 184 </ol> --> 185 </div> 186 </div> 187 </div> 188 189 <div class="item"> 190 <div class="head d-flex justify-content-between align-items-center"> 191 <h2 class="mb-0 flex-grow-1">How does CIPRES support its users?</h2> 192 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 193 </div> 194 <div class="block"> 195 <div class="fold-content"> 196 <p><strong>We are committed to providing excellent user support.</strong><br /> 197Our team is small, so perfection is not possible. But we are eager to learn about and attend to any issues users encounter.<br /> 198Support is available (minimally) M-F 9 AM - 5 PM Pacific Time. Response time is typically 2-4 hours during that time.</p> 199 200<p><strong>Bugs/Job Issues:</strong><br /> 201We encourage users to report issues through our <a href="https://groups.google.com/g/cipres-science-gateway-users" target="_blank">Google Group</a>.</p> 202 203<p><strong>Custom help is available:</strong><br /> 204Our team is highly experienced in running community HPC codes successfully. We are happy to work with individual users to provide advice, make new features and codes available, and to customize runs to meet user needs whenever possible. <br /> 205 </p> 206 <!-- <p>There are two ways a registration might fail:</p> 207 <ol> 208 <li>You registered successfully, but did not receive an activation email. Globally servers are very concerned about SPAM and pfishing, so our activation email occasionally does not make it to the user. If you don't see the email in your personal SPAM catcher, it is best to just contact us, and we will activate on our side.</li> 209 <li>You tried to register, but received a warning that your registration could not be completed. This may happen because CIPRES does not allow a user to hold multiple accounts. The application automatically prevents registration of a second account by a single user. If you see this message, just contact us through the email referenced in the message. We can help.</li> 210 </ol> --> 211 </div> 212 </div>
213 </div> 214 215 <div class="item"> 216 <div class="head d-flex justify-content-between align-items-center"> 217 <h2 class="mb-0 flex-grow-1">Can I monitor results in real time?</h2> 218 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 219 </div> 220 <div class="block"> 221 <div class="fold-content"> 222 <table border="0" style="width:1200px"> 223 <tbody> 224 <tr> 225 <td> 226 <p><strong>Intermediate Results:</strong> CIPRES makes it possible to view intermediate results so you can follow the progress of your job. You can (and are encouraged to) monitor the progress of long runs. To view intermediate results for a running job, click on the "View Status" button. When that page opens, you will see an "Intermediate results" hyperlink. Click it and you and a pop-up will appear that displays all input files and any results for the selected job. The intermediate results pane shows input files and scheduling information files immediately, so you can make sure everything looks fine before the job begins. When the job initiates (normally within a few minutes), more files will appear, beginning with start.txt. The start.txt file notes the time when the job began executing. More details are provided <a href="https://www.phylo.org/index.php/help/progress">here</a></p> 227 228 <p><strong>How do I know if my job has started?</strong> If the job has not started, the intermediate results pane shows only input files and scheduling files. This means your job is still waiting in the queue. Jobs usually (but not always) start within 15 minutes. You can keep the intermediate file page open and refresh from time to time to see when the start.txt file appears.</p> 229 230 <p><strong>What if the queue time seems long?</strong> If the queue time seems long, there are two possible reasons.<br /> 231 First, and most likely, the queue may be paused because of a scheduled or unscheduled maintenance. Typically, when a maintenance occurs, we will post a message on the front page. The (normally green) status box will turn red, with an informative message. You can also check for scheduled maintenance events <a href="https://support.access-ci.org/outages">here</a>; or just contact us at the link below if you aren't sure. Any job that might be still running into the maintenance period will be held in the queue until maintenance is complete. Once maintenance completes, the job should initiate within an hour or so. If it does not, you should contact us at the link below. Occasionally (but rarely) a job does not come out of maintenance cleanly, so it is possible that your job will hang.</p> 232 233 <p>Second, and less likely, the queue might actually be long, and it could take hours for the job to start. If you have a paid subscription, jobs configured to run for 6 hours or less will be placed in a dedicated queue, and should start instantly. If you have questions, please contact us.</p> 234 </td> 235 </tr> 236 </tbody> 237</table> 238 <!-- <p>There are two ways a registration might fail:</p> 239 <ol> 240 <li>You registered successfully, but did not receive an activation email. Globally servers are very concerned about SPAM and pfishing, so our activation email occasionally does not make it to the user. If you don't see the email in your personal SPAM catcher, it is best to just contact us, and we will activate on our side.</li> 241 <li>You tried to register, but received a warning that your registration could not be completed. This may happen because CIPRES does not allow a user to hold multiple accounts. The application automatically prevents registration of a second account by a single user. If you see this message, just contact us through the email referenced in the message. We can help.</li> 242 </ol> --> 243 </div> 244 </div> 245 </div> 246 247 <div class="item"> 248 <div class="head d-flex justify-content-between align-items-center"> 249 <h2 class="mb-0 flex-grow-1">My job died, now what?</h2> 250 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 251 </div> 252 <div class="block"> 253 <div class="fold-content"> 254 <p>
254If your job fails immediately, or dies unexpectedly, first, please do not delete the job from your interface.<br /> 255Try using the <a href="https://www.phylo.org/inner-pages/support-detail/troubleshooting-job-runs">help tools</a> to troubleshoot the issue, and if you can't figure it out, report the failure to us. Here is <a href="https://www.phylo.org/index.php/help/report_failed_job">how.</a></p> 256 257<p>A <a href="http://www.phylo.org/tools/html5/troubleshoot_demo/index.html">troubleshooting video</a> is available.</p> 258 259<p>We will happily credit your account for any loss due to an issue on our side.</p> 260 261<p><a href="https://www.phylo.org/index.php/help/report_failed_job"> </a></p> 262 <!-- <p>There are two ways a registration might fail:</p> 263 <ol> 264 <li>You registered successfully, but did not receive an activation email. Globally servers are very concerned about SPAM and pfishing, so our activation email occasionally does not make it to the user. If you don't see the email in your personal SPAM catcher, it is best to just contact us, and we will activate on our side.</li> 265 <li>You tried to register, but received a warning that your registration could not be completed. This may happen because CIPRES does not allow a user to hold multiple accounts. The application automatically prevents registration of a second account by a single user. If you see this message, just contact us through the email referenced in the message. We can help.</li> 266 </ol> --> 267 </div> 268 </div> 269 </div> 270 271 <div class="item"> 272 <div class="head d-flex justify-content-between align-items-center"> 273 <h2 class="mb-0 flex-grow-1">My job completed, but I don't see an output tree</h2> 274 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 275 </div> 276 <div class="block"> 277 <div class="fold-content"> 278 <p><strong>What if the job completes and I don't see my tree?</strong></p> 279 280<p>There are basically two reasons this might happen that are in your control.</p> 281 282<p>The most common reason for a job failure is that the code did not like your input files or your command line choices. To diagnose this, have a look at the last few lines of the stdout.txt and stderr.txt files. Most of the codes we support provde notice of a failure a useful and human readable statement of the failure case. You can ask us for help if you cant make sense of the message.</p> 283 284<p>The second common reason for a file not appearing is the job reached its wall time limit before it completed. If there is no obvious error message in stderr.txt or stdout.txt, look next at the file _scheduler_stderr.txt. If the job did not complete in the allotted time, it will contain a message like this: slurmstepd: error: *** STEP 23338670.0 ON exp-1-43 CANCELLED AT 2023-06-23T15:01:48 DUE TO TIME LIMIT ***.</p> 285 286<p>To handle this, see "restarting jobs".</p> 287 288<p>If you don't see evidence of either of the above, most likely the job failed due to a transient system problem (this should be rare), or a specific known issue with the code (see the text for specific codes below). <em><strong>Please report </strong></em>any jobs that fail to produce the expected results.</p> 289 290<p>A <a href="http://www.phylo.org/tools/html5/troubleshoot_demo/index.html">troubleshooting video</a> is available.</p> 291 <!-- <p>There are two ways a registration might fail:</p> 292 <ol> 293 <li>You registered successfully, but did not receive an activation email. Globally servers are very concerned about SPAM and pfishing, so our activation email occasionally does not make it to the user. If you don't see the email in your personal SPAM catcher, it is best to just contact us, and we will activate on our side.</li> 294 <li>You tried to register, but received a warning that your registration could not be completed. This may happen because CIPRES does not allow a user to hold multiple accounts. The application automatically prevents registration of a second account by a single user. If you see this message, just contact us through the email referenced in the message. We can help.</li> 295 </ol> --> 296 </div> 297 </div>
298 </div> 299 300 <div class="item"> 301 <div class="head d-flex justify-content-between align-items-center"> 302 <h2 class="mb-0 flex-grow-1">My job didn't complete, can it be restarted?</h2> 303 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 304 </div> 305 <div class="block"> 306 <div class="fold-content"> 307 <p><strong>My job didn't complete, can it be restarted?</strong></p> 308 309<p><strong>Restarting Jobs: </strong>If it is supported, you can "restart" a job that "timed out". If a job can be restarted, a "restart" button will appear next to the "clone" button. You may have to "refresh" the page using the button at the top right of the jobs list page. Just click the restart button, and the job will run again for the same amount of time you originally configured. The interface will allow you to review and alter many parameters. The following codes can be restarted on this way: BEAST, BEAST2, MrBayes, IQ-Tree, ExaBayes, IMa3, RAxMLNG, PhyloBayes.</p> 310 311<p><strong>Special Restart Interfaces:</strong> You can restart MrBayes using a specific restart interface. These interfaces are more tedious, but will work.</p> 312 313<p><strong>No Restart Option: </strong>If your code does not support restarts, your main option is to "clone" the job, and re-run, using the parameter pane to increase the maximum allowed run time. If you need to run longer than our maximum allowed time, all is not lost, please contact us for help and advice.</p> 314 <!-- <p>There are two ways a registration might fail:</p> 315 <ol> 316 <li>You registered successfully, but did not receive an activation email. Globally servers are very concerned about SPAM and pfishing, so our activation email occasionally does not make it to the user. If you don't see the email in your personal SPAM catcher, it is best to just contact us, and we will activate on our side.</li> 317 <li>You tried to register, but received a warning that your registration could not be completed. This may happen because CIPRES does not allow a user to hold multiple accounts. The application automatically prevents registration of a second account by a single user. If you see this message, just contact us through the email referenced in the message. We can help.</li> 318 </ol> --> 319 </div> 320 </div> 321 </div> 322 323 <div class="item"> 324 <div class="head d-flex justify-content-between align-items-center"> 325 <h2 class="mb-0 flex-grow-1">How do you handle maintenance?</h2> 326 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 327 </div> 328 <div class="block"> 329 <div class="fold-content"> 330 <table border="0" style="width:1200px"> 331 <tbody> 332 <tr> 333 <td> 334 <p>All complex HPC resources must undergo maintenance from time to time. Our goal at CIPRES is to minimize the risk to your allocation time. Maintenance periods are typically planned and scheduled in advance, but (rarely) an emergency situation arises, and the resource must be shut down unexpectedly. When a maintenance period is required, the queue is paused because the maintenance will kill running jobs. Any job that might be still running into the maintenance period will be held in the queue until maintenance is complete. We notify users of planned maintenance, or ongoing maintenance using a status box on the front page. The (normally green) status box will turn red, and provide an informative message. Please contact us at the link below if you have questions.</p> 335 336 <p>During any maintenance period, submissions will be paused (though your job can be saved for later deployment). Once maintenance completes, the job should initiate within an hour or so. If it does not, you should contact us at the link below. In the event of emergency maintence that kills a running job, please contact us to refund time to your account.</p> 337 338 <p><em><strong>If you are running a restartable job,</strong></em> you can work through a coming maintenance period by shortening your maximum run time, so it does not enter the maintenance peri
338od. If the run ends before it is complete, you can restart and complete the job once maintenance is over. Just be sure your job is restartable.</p> 339 </td> 340 </tr> 341 </tbody> 342</table> 343 <!-- <p>There are two ways a registration might fail:</p> 344 <ol> 345 <li>You registered successfully, but did not receive an activation email. Globally servers are very concerned about SPAM and pfishing, so our activation email occasionally does not make it to the user. If you don't see the email in your personal SPAM catcher, it is best to just contact us, and we will activate on our side.</li> 346 <li>You tried to register, but received a warning that your registration could not be completed. This may happen because CIPRES does not allow a user to hold multiple accounts. The application automatically prevents registration of a second account by a single user. If you see this message, just contact us through the email referenced in the message. We can help.</li> 347 </ol> --> 348 </div> 349 </div> 350 </div> 351 352 <div class="item"> 353 <div class="head d-flex justify-content-between align-items-center"> 354 <h2 class="mb-0 flex-grow-1">What parallel codes does CIPRES offer?</h2> 355 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 356 </div> 357 <div class="block"> 358 <div class="fold-content"> 359 <h3><strong>Parallel tools currently supported by the CIPRES Science Gateway can be found <a href="https://www.phylo.org/index.php/portal/codes">here</a>.</strong></h3> 360 361<p>*GPUs are charged as 20 cpu cores. So a 4 GPU run will be charged as 4 * 20 = 80 cpu cores per hour.</p> 362 <!-- <p>There are two ways a registration might fail:</p> 363 <ol> 364 <li>You registered successfully, but did not receive an activation email. Globally servers are very concerned about SPAM and pfishing, so our activation email occasionally does not make it to the user. If you don't see the email in your personal SPAM catcher, it is best to just contact us, and we will activate on our side.</li> 365 <li>You tried to register, but received a warning that your registration could not be completed. This may happen because CIPRES does not allow a user to hold multiple accounts. The application automatically prevents registration of a second account by a single user. If you see this message, just contact us through the email referenced in the message. We can help.</li> 366 </ol> --> 367 </div> 368 </div> 369 </div> 370 371 <div class="item"> 372 <div class="head d-flex justify-content-between align-items-center"> 373 <h2 class="mb-0 flex-grow-1">What serial codes does CIPRES offer?</h2> 374 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 375 </div> 376 <div class="block"> 377 <div class="fold-content"> 378 <h3><strong>Serial tools currently supported by the CIPRES Science Gateway. We also support several utilities, such as READSEQ, NCL-Converter for file transformation. All of these codes run on a single core. </strong></h3> 379 380<table border="1" cellpadding="1" cellspacing="1" style="height:228px; width:378px"> 381 <tbody> 382 <tr> 383 <td style="text-align:center"><strong>Tool</strong></td> 384 <td style="text-align:center"><strong>Version</strong></td> 385 <td style="text-align:center"><strong>Language</strong></td> 386 <td style="text-align:center"><strong>Compiler</strong></td> 387 <td style="text-align:center"><strong>Cluster</strong></td> 388 </tr> 389 <tr> 390 <td style="text-align:center">ClustalW</td> 391 <td style="text-align:center">2.1</td> 392 <td style="text-align:center">C/C++</td> 393 <td style="text-align:center">Clang</td> 394 <td style="text-align:center">Expanse</td> 395 </tr> 396 <tr> 397 <td style="text-align:center">Divvier</td> 398 <td style="text-align:center">1.0.1</td> 399 <td style="text-align:center">C/C++</td> 400 <td style="text-align:center">GNU</td> 401 <td style="text-align:center">Expanse</td> 402 </tr> 403 <tr> 404 <td style="text-align:center">MPBOOT</td> 405 <td style="text-align:center">1.2</td> 406 <td style="text-align:center">C/C++</td> 407 <td style="text-align:center">GNU</td> 408 <td style="text-align:center">Expanse</td> 409 </tr> 410 <tr> 411 <td style="text-align:center">PREQUAL</td> 412 <td style="text-align:center">1.02</td> 413 <td style="text-align:center">C/C++</td> 414 <td style="text-align:center">GNU</td> 415 <td style="text-align:center">Expanse</td> 416 </tr> 417 <tr> 418 <td style="text-align:center">PROBCONS</td> 419 <td style="text-align:center">1.12</td> 420 <td style="text-align:center">C/C++</td> 421 <td style="text-align:center">GNU</td> 422 <td style="text-align:center">Expanse</td> 423 </tr> 424 <tr> 425 <td style="text-align:center">PROBALIGN</td> 426 <td style="text-align:center">1.3</td> 427 <td style="text-align:center">C/C++</td> 428 <td style="text-align:center">GNU</td> 429 <td style="text-align:center">Expanse</td> 430 </tr> 431 </tbody> 432</table> 433 <!-- <p>There are two ways a registration might fail:</p> 434 <ol> 435 <li>You registered successfully, but did not receive an activation email. Globally servers are very concerned about SPAM and pfishing, so our activation email occasionally does not make it to the user. If you don't see the email in your personal SPAM catcher, it is best to just contact us, and we will activate on our side.</li> 436 <li>You tried to register, but received a warning that your registration could not be completed. This may happen because CIPRES does not allow a user to hold multiple accounts. The application automatically prevents registration of a second account by a single user. If you see this message, just contact us through the email referenced in the message. We can help.</li> 437 </ol> --> 438 </div> 439 </div>
440 </div> 441 442 <div class="item"> 443 <div class="head d-flex justify-content-between align-items-center"> 444 <h2 class="mb-0 flex-grow-1">How can I subscribe?</h2> 445 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 446 </div> 447 <div class="block"> 448 <div class="fold-content"> 449 <p><strong>We regret we can no longer offer subscriptions. You can still create an account and use the available time through 3/31.2026. If you have an account and need more time, please dont mae a new account, contact us.</strong></p> 450 <!-- <p>There are two ways a registration might fail:</p> 451 <ol> 452 <li>You registered successfully, but did not receive an activation email. Globally servers are very concerned about SPAM and pfishing, so our activation email occasionally does not make it to the user. If you don't see the email in your personal SPAM catcher, it is best to just contact us, and we will activate on our side.</li> 453 <li>You tried to register, but received a warning that your registration could not be completed. This may happen because CIPRES does not allow a user to hold multiple accounts. The application automatically prevents registration of a second account by a single user. If you see this message, just contact us through the email referenced in the message. We can help.</li> 454 </ol> --> 455 </div> 456 </div> 457 </div> 458 459 <div class="item"> 460 <div class="head d-flex justify-content-between align-items-center"> 461 <h2 class="mb-0 flex-grow-1">I have a question about how subscriptions work</h2> 462 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 463 </div> 464 <div class="block"> 465 <div class="fold-content"> 466 <h2><strong>CIPRES Subscriptions: Frequently Asked Questions</strong></h2> 467 468<p><strong>We regret we can no longer offer subscriptions. If you have an account and need more time, please dont make an account, contact us.</strong></p> 469 470<p><!--[endif]----></p> 471 <!-- <p>There are two ways a registration might fail:</p> 472 <ol> 473 <li>You registered successfully, but did not receive an activation email. Globally servers are very concerned about SPAM and pfishing, so our activation email occasionally does not make it to the user. If you don't see the email in your personal SPAM catcher, it is best to just contact us, and we will activate on our side.</li> 474 <li>You tried to register, but received a warning that your registration could not be completed. This may happen because CIPRES does not allow a user to hold multiple accounts. The application automatically prevents registration of a second account by a single user. If you see this message, just contact us through the email referenced in the message. We can help.</li> 475 </ol> --> 476 </div> 477 </div> 478 </div> 479 480 <div class="item"> 481 <div class="head d-flex justify-content-between align-items-center"> 482 <h2 class="mb-0 flex-grow-1">Where can I get the CIPRES Software?</h2> 483 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 484 </div> 485 <div class="block"> 486 <div class="fold-content"> 487 <p>The software for the CIPRES Workbench framework is <a href="https://svn2.sdsc.edu/repo/NGBW/" target="_blank">freely available.</a><br /> 488Instructions can be found <a href="https://svn.sdsc.edu/repo/scigap/trunk/documents/framework_install.txt" target="_blank">here.</a><br /> 489The paper describing the software is available <a href="https://www.phylo.org/system/uploads/cipres_xsede2015_fin.pdf" target="_blank">here</a></p> 490 <!-- <p>There are two ways a registration might fail:</p> 491 <ol> 492 <li>You registered successfully, but did not receive an activation email. Globally servers are very concerned about SPAM and pfishing, so our activation email occasionally does not make it to the user. If you don't see the email in your personal SPAM catcher, it is best to just contact us, and we will activate on our side.</li> 493 <li>You tried to register, but received a warning that your registration could not be completed. This may happen because CIPRES does not allow a user to hold multiple accounts. The application automatically prevents registration of a second account by a single user. If you see this message, just contact us through the email referenced in the message. We can help.</li> 494 </ol> --> 495 </div> 496 </div>
497 </div> 498 499 <div class="item"> 500 <div class="head d-flex justify-content-between align-items-center"> 501 <h2 class="mb-0 flex-grow-1">How do I cite CIPRES</h2> 502 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 503 </div> 504 <div class="block"> 505 <div class="fold-content"> 506 <p>If you use the resources available from the CIPRES Science Gateway to complete published work, please cite us as follows: <strong>Miller, M.A., Pfeiffer, W., and Schwartz, T. (2010) "Creating the CIPRES Science Gateway for inference of large phylogenetic trees" in Proceedings of the Gateway Computing Environments Workshop (GCE), 14 Nov. 2010, New Orleans, LA pp 1 - 8. DOI: 10.1109/GCE.2010.5676129 <a href="http://www.phylo.org/sub_sections/portal/sc2010_paper.pdf"> PDF</a></strong>.</p> 507 <!-- <p>There are two ways a registration might fail:</p> 508 <ol> 509 <li>You registered successfully, but did not receive an activation email. Globally servers are very concerned about SPAM and pfishing, so our activation email occasionally does not make it to the user. If you don't see the email in your personal SPAM catcher, it is best to just contact us, and we will activate on our side.</li> 510 <li>You tried to register, but received a warning that your registration could not be completed. This may happen because CIPRES does not allow a user to hold multiple accounts. The application automatically prevents registration of a second account by a single user. If you see this message, just contact us through the email referenced in the message. We can help.</li> 511 </ol> --> 512 </div> 513 </div> 514 </div> 515 516<!-- <div class="item"> 517 <div class="head d-flex justify-content-between align-items-center"> 518 <h2 class="mb-0 flex-grow-1">Where can I learn how to use CIPRES?</h2> 519 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 520 </div> 521 <div class="block"> 522 <div class="fold-content"> 523 <p> 524 Lorem ipsum dolor sit amet consectetur adipisicing elit. Inventore, consequuntur laboriosam quia ullam numquam magnam iure sint placeat eveniet. Illum quod odit est aliquid corporis nostrum, quas molestias vel praesentium ducimus incidunt, excepturi quia, distinctio repellendus officia totam sit natus! Reprehenderit doloribus ab quibusdam vero obcaecati alias tempore dolorum odit accusamus. Praesentium inventore aspernatur necessitatibus assumenda magnam delectus nisi modi qui, architecto recusandae commodi a, ratione veritatis nam dolor, eos eligendi ipsum id minima. Quasi dignissimos debitis iure amet ut? At labore 525 iste voluptas tempore itaque asperiores rem recusandae, cum, voluptates architecto unde eligendi repellendus animi quaerat eveniet id! Maiores et consequatur ipsum voluptas voluptatibus possimus nostrum doloremque porro cupiditate labore libero ad optio atque, amet quas. Quisquam, illo fugiat! 526 </p> 527 </div> 528 </div> 529 </div> 530 <div class="item"> 531 <div class="head d-flex justify-content-between align-items-center"> 532 <h2 class="mb-0 flex-grow-1">How does CIPRES support its users?</h2> 533 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 534 </div> 535 <div class="block"> 536 <div class="fold-content"> 537 <p> 538 Lorem ipsum dolor sit amet consectetur adipisicing elit. Inventore, consequuntur laboriosam quia ullam numquam magnam iure sint placeat eveniet. Illum quod odit est aliquid corporis nostrum, quas molestias vel praesentium ducimus incidunt, excepturi quia, distinctio repellendus officia totam sit natus! Reprehenderit doloribus ab quibusdam vero obcaecati alias tempore dolorum odit accusamus. Praesentium inventore aspernatur necessitatibus assumenda magnam delectus nisi modi qui, architecto recusandae commodi a, ratione veritatis nam dolor, eos eligendi ipsum id minima. Quasi dignissimos debitis iure amet ut? At labore 539 iste voluptas tempore itaque asperiores rem recusandae, cum, voluptates architecto unde eligendi repellendus animi quaerat eveniet id! Maiores et consequatur ipsum voluptas voluptatibus possimus nostrum doloremque porro cupiditate labore libero ad optio atque, amet quas. Qu
539isquam, illo fugiat! 540 </p> 541 </div> 542 </div> 543 </div> 544 <div class="item"> 545 <div class="head d-flex justify-content-between align-items-center"> 546 <h2 class="mb-0 flex-grow-1">Can I monitor results in real time?</h2> 547 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 548 </div> 549 <div class="block"> 550 <div class="fold-content"> 551 <p> 552 Lorem ipsum dolor sit amet consectetur adipisicing elit. Inventore, consequuntur laboriosam quia ullam numquam magnam iure sint placeat eveniet. Illum quod odit est aliquid corporis nostrum, quas molestias vel praesentium ducimus incidunt, excepturi quia, distinctio repellendus officia totam sit natus! Reprehenderit doloribus ab quibusdam vero obcaecati alias tempore dolorum odit accusamus. Praesentium inventore aspernatur necessitatibus assumenda magnam delectus nisi modi qui, architecto recusandae commodi a, ratione veritatis nam dolor, eos eligendi ipsum id minima. Quasi dignissimos debitis iure amet ut? At labore 553 iste voluptas tempore itaque asperiores rem recusandae, cum, voluptates architecto unde eligendi repellendus animi quaerat eveniet id! Maiores et consequatur ipsum voluptas voluptatibus possimus nostrum doloremque porro cupiditate labore libero ad optio atque, amet quas. Quisquam, illo fugiat! 554 </p> 555 </div> 556 </div> 557 </div> 558 <div class="item"> 559 <div class="head d-flex justify-content-between align-items-center"> 560 <h2 class="mb-0 flex-grow-1">What if my job doesn't start?</h2> 561 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 562 </div> 563 <div class="block"> 564 <div class="fold-content"> 565 <p> 566 Lorem ipsum dolor sit amet consectetur adipisicing elit. Inventore, consequuntur laboriosam quia ullam numquam magnam iure sint placeat eveniet. Illum quod odit est aliquid corporis nostrum, quas molestias vel praesentium ducimus incidunt, excepturi quia, distinctio repellendus officia totam sit natus! Reprehenderit doloribus ab quibusdam vero obcaecati alias tempore dolorum odit accusamus. Praesentium inventore aspernatur necessitatibus assumenda magnam delectus nisi modi qui, architecto recusandae commodi a, ratione veritatis nam dolor, eos eligendi ipsum id minima. Quasi dignissimos debitis iure amet ut? At labore 567 iste voluptas tempore itaque asperiores rem recusandae, cum, voluptates architecto unde eligendi repellendus animi quaerat eveniet id! Maiores et consequatur ipsum voluptas voluptatibus possimus nostrum doloremque porro cupiditate labore libero ad optio atque, amet quas. Quisquam, illo fugiat! 568 </p> 569 </div> 570 </div> 571 </div> 572 <div class="item"> 573 <div class="head d-flex justify-content-between align-items-center"> 574 <h2 class="mb-0 flex-grow-1">My job died, now what?</h2> 575 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 576 </div> 577 <div class="block"> 578 <div class="fold-content"> 579 <p> 580 Lorem ipsum dolor sit amet consectetur adipisicing elit. Inventore, consequuntur laboriosam quia ullam numquam magnam iure sint placeat eveniet. Illum quod odit est aliquid corporis nostrum, quas molestias vel praesentium ducimus incidunt, excepturi quia, distinctio repellendus officia totam sit natus! Reprehenderit doloribus ab quibusdam vero obcaecati alias tempore dolorum odit accusamus. Praesentium inventore aspernatur necessitatibus assumenda magnam delectus nisi modi qui, architecto recusandae commodi a, ratione veritatis nam dolor, eos eligendi ipsum id minima. Quasi dignissimos debitis iure amet ut? At labore 581 iste voluptas tempore itaque asperiores rem recusandae, cum, voluptates architecto unde eligendi repellendus animi quaerat eveniet id! Maiores et consequatur ipsum voluptas voluptatibus possimus nostrum doloremque porro cupiditate labore libero ad optio atque, amet quas. Quisquam, illo fugiat! 582 </p> 583 </div> 584 </div> 585 </div> 586 <div class="item"> 587 <div class="head d-flex justify-content-between align-items-center"> 588 <h2 class="mb-0 flex-grow-1">My job completed, but I don't see an output tree</h2> 589 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 590 </div> 591 <div class="block"> 592 <div class="fold-content"> 593 <p> 594 Lorem ipsum dolor sit amet consectetur adipisicing elit. Inventore, consequuntur laboriosam quia ullam numquam magnam iure sint placeat eveniet. Illum quod odit est aliquid corporis nostrum, quas molestias vel praesentium ducimus incidunt, excepturi quia, distinctio repellendus officia totam sit natus! Reprehenderit doloribus ab quibusdam vero obcaecati alias tempore dolorum odit accusamus. Praesentium inventore aspernatur necessitatibus assumenda magnam delectus nisi modi qui, architecto recusandae commodi a, ratione veritatis nam dolor, eos eligendi ipsum id minima. Quasi dignissimos debitis iure amet ut? At labore 595 iste voluptas tempore itaque asperiores rem recusandae, cum, voluptates architecto unde eligendi repellendus animi quaerat eveniet id! Maiores et consequatur ipsum voluptas voluptatibus possimus nostrum doloremque porro cupiditate labore libero ad optio atque, amet quas. Qu
595isquam, illo fugiat! 596 </p> 597 </div> 598 </div> 599 </div> 600 <div class="item"> 601 <div class="head d-flex justify-content-between align-items-center"> 602 <h2 class="mb-0 flex-grow-1">Help, my job hit the time limit!</h2> 603 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 604 </div> 605 <div class="block"> 606 <div class="fold-content"> 607 <p> 608 Lorem ipsum dolor sit amet consectetur adipisicing elit. Inventore, consequuntur laboriosam quia ullam numquam magnam iure sint placeat eveniet. Illum quod odit est aliquid corporis nostrum, quas molestias vel praesentium ducimus incidunt, excepturi quia, distinctio repellendus officia totam sit natus! Reprehenderit doloribus ab quibusdam vero obcaecati alias tempore dolorum odit accusamus. Praesentium inventore aspernatur necessitatibus assumenda magnam delectus nisi modi qui, architecto recusandae commodi a, ratione veritatis nam dolor, eos eligendi ipsum id minima. Quasi dignissimos debitis iure amet ut? At labore 609 iste voluptas tempore itaque asperiores rem recusandae, cum, voluptates architecto unde eligendi repellendus animi quaerat eveniet id! Maiores et consequatur ipsum voluptas voluptatibus possimus nostrum doloremque porro cupiditate labore libero ad optio atque, amet quas. Quisquam, illo fugiat! 610 </p> 611 </div> 612 </div> 613 </div> 614 <div class="item"> 615 <div class="head d-flex justify-content-between align-items-center"> 616 <h2 class="mb-0 flex-grow-1">How do you handle maintenance?</h2> 617 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 618 </div> 619 <div class="block"> 620 <div class="fold-content"> 621 <p> 622 Lorem ipsum dolor sit amet consectetur adipisicing elit. Inventore, consequuntur laboriosam quia ullam numquam magnam iure sint placeat eveniet. Illum quod odit est aliquid corporis nostrum, quas molestias vel praesentium ducimus incidunt, excepturi quia, distinctio repellendus officia totam sit natus! Reprehenderit doloribus ab quibusdam vero obcaecati alias tempore dolorum odit accusamus. Praesentium inventore aspernatur necessitatibus assumenda magnam delectus nisi modi qui, architecto recusandae commodi a, ratione veritatis nam dolor, eos eligendi ipsum id minima. Quasi dignissimos debitis iure amet ut? At labore 623 iste voluptas tempore itaque asperiores rem recusandae, cum, voluptates architecto unde eligendi repellendus animi quaerat eveniet id! Maiores et consequatur ipsum voluptas voluptatibus possimus nostrum doloremque porro cupiditate labore libero ad optio atque, amet quas. Quisquam, illo fugiat! 624 </p> 625 </div> 626 </div> 627 </div> 628 <div class="item"> 629 <div class="head d-flex justify-content-between align-items-center"> 630 <h2 class="mb-0 flex-grow-1">What parallel codes does CIPRES offer?</h2> 631 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 632 </div> 633 <div class="block"> 634 <div class="fold-content"> 635 <p> 636 Lorem ipsum dolor sit amet consectetur adipisicing elit. Inventore, consequuntur laboriosam quia ullam numquam magnam iure sint placeat eveniet. Illum quod odit est aliquid corporis nostrum, quas molestias vel praesentium ducimus incidunt, excepturi quia, distinctio repellendus officia totam sit natus! Reprehenderit doloribus ab quibusdam vero obcaecati alias tempore dolorum odit accusamus. Praesentium inventore aspernatur necessitatibus assumenda magnam delectus nisi modi qui, architecto recusandae commodi a, ratione veritatis nam dolor, eos eligendi ipsum id minima. Quasi dignissimos debitis iure amet ut? At labore 637 iste voluptas tempore itaque asperiores rem recusandae, cum, voluptates architecto unde eligendi repellendus animi quaerat eveniet id! Maiores et consequatur ipsum voluptas voluptatibus possimus nostrum doloremque porro cupiditate labore libero ad optio atque, amet quas. Quisquam, illo fugiat! 638 </p> 639 </div> 640 </div>
641 </div> 642 <div class="item"> 643 <div class="head d-flex justify-content-between align-items-center"> 644 <h2 class="mb-0 flex-grow-1">What serial codes does CIPRES offer?</h2> 645 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 646 </div> 647 <div class="block"> 648 <div class="fold-content"> 649 <p> 650 Lorem ipsum dolor sit amet consectetur adipisicing elit. Inventore, consequuntur laboriosam quia ullam numquam magnam iure sint placeat eveniet. Illum quod odit est aliquid corporis nostrum, quas molestias vel praesentium ducimus incidunt, excepturi quia, distinctio repellendus officia totam sit natus! Reprehenderit doloribus ab quibusdam vero obcaecati alias tempore dolorum odit accusamus. Praesentium inventore aspernatur necessitatibus assumenda magnam delectus nisi modi qui, architecto recusandae commodi a, ratione veritatis nam dolor, eos eligendi ipsum id minima. Quasi dignissimos debitis iure amet ut? At labore 651 iste voluptas tempore itaque asperiores rem recusandae, cum, voluptates architecto unde eligendi repellendus animi quaerat eveniet id! Maiores et consequatur ipsum voluptas voluptatibus possimus nostrum doloremque porro cupiditate labore libero ad optio atque, amet quas. Quisquam, illo fugiat! 652 </p> 653 </div> 654 </div> 655 </div> 656 <div class="item"> 657 <div class="head d-flex justify-content-between align-items-center"> 658 <h2 class="mb-0 flex-grow-1">How can I subscribe?</h2> 659 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 660 </div> 661 <div class="block"> 662 <div class="fold-content"> 663 <p> 664 Lorem ipsum dolor sit amet consectetur adipisicing elit. Inventore, consequuntur laboriosam quia ullam numquam magnam iure sint placeat eveniet. Illum quod odit est aliquid corporis nostrum, quas molestias vel praesentium ducimus incidunt, excepturi quia, distinctio repellendus officia totam sit natus! Reprehenderit doloribus ab quibusdam vero obcaecati alias tempore dolorum odit accusamus. Praesentium inventore aspernatur necessitatibus assumenda magnam delectus nisi modi qui, architecto recusandae commodi a, ratione veritatis nam dolor, eos eligendi ipsum id minima. Quasi dignissimos debitis iure amet ut? At labore 665 iste voluptas tempore itaque asperiores rem recusandae, cum, voluptates architecto unde eligendi repellendus animi quaerat eveniet id! Maiores et consequatur ipsum voluptas voluptatibus possimus nostrum doloremque porro cupiditate labore libero ad optio atque, amet quas. Quisquam, illo fugiat! 666 </p> 667 </div> 668 </div> 669 </div> 670 <div class="item"> 671 <div class="head d-flex justify-content-between align-items-center"> 672 <h2 class="mb-0 flex-grow-1">I have a question about how subscriptions work</h2> 673 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 674 </div> 675 <div class="block"> 676 <div class="fold-content"> 677 <p> 678 Lorem ipsum dolor sit amet consectetur adipisicing elit. Inventore, consequuntur laboriosam quia ullam numquam magnam iure sint placeat eveniet. Illum quod odit est aliquid corporis nostrum, quas molestias vel praesentium ducimus incidunt, excepturi quia, distinctio repellendus officia totam sit natus! Reprehenderit doloribus ab quibusdam vero obcaecati alias tempore dolorum odit accusamus. Praesentium inventore aspernatur necessitatibus assumenda magnam delectus nisi modi qui, architecto recusandae commodi a, ratione veritatis nam dolor, eos eligendi ipsum id minima. Quasi dignissimos debitis iure amet ut? At labore 679 iste voluptas tempore itaque asperiores rem recusandae, cum, voluptates architecto unde eligendi repellendus animi quaerat eveniet id! Maiores et consequatur ipsum voluptas voluptatibus possimus nostrum doloremque porro cupiditate labore libero ad optio atque, amet quas. Quisquam, illo fugiat! 680 </p> 681 </div> 682 </div> 683 </div> 684 <div class="item"> 685 <div class="head d-flex justify-content-between align-items-center"> 686 <h2 class="mb-0 flex-grow-1">Where can I get the CIPRES Software?</h2> 687 <div class="icon ms-3 d-flex"><img src="images/fold-arrow.svg" alt="" height="20" width="20" /></div> 688 </div> 689 <div class="block"> 690 <div class="fold-content"> 691 <p> 692 Lorem ipsum dolor sit amet consectetur adipisicing elit. 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