Following up on my previous setup of syncing external data backups, and my fears of bitrot gradually rising as my data becomes more fragmented, more at rest, and also more subject to frequently copy over sometimes non-ECC RAM, I’m moving to ZFS, which is nothing short of magic, on my external …

It is just wonderful when you start the morning with your system booting into a kernel panic. Loading, please wait... /init: conf/conf.d/zz-resume-auto: line 1: syntax error: unexpected "(" Kernel panic - not syncing: Attempted to kill init! exitcode=0x00000200 It looks like my initramfs has …

In this age, storage is cheap. Data, however, is not. As is tradition for every quarter I make backups of all my important data onto a trusty external hard drive, and as a proponent of the 3-2-1 backup rule, I have to sync my backup to other drives for safekeeping. The problem at hand is then: Given …

Recently my virtual machine setup under a Linux host (Kernel 5.13.0) has been plagued by extreme lagginess to the point of being unusable. Checking top shows that vmware-vmx is using all the CPU that is allocated to the VM, but the VM does not respond. Things I tried that didn’t work: Disable …

Preface I’ve recently decommissioned a (not so old) laptop to make room. The laptop’s old hard drive (actually a NVMe) was removed and put into an external enclosure, so I didn’t have to deal with moving all data from it, wiping the drive, and realizing I left something in an …

Don’t you hate it when you have to reach for 2FA or the password manager again and again when transferring multiple files over scp or opening an extra ssh session because your cluster’s ls command froze again? Turns out that ssh can keep it alive for you! A ControlMaster feature can be …

We’ve been receiving lots of questions from WRF-GC users regarding whether it’s possible for WRF-GC to output custom quantities, such as internal diagnostic quantities in GEOS-Chem or HEMCO. The answer is, maybe. It is important to remember that, as described in the model description …

Recently I’ve ran into an issue where my WRF nudging runs are so long that OBSGRID cannot correctly generate the wrfsfdda_d0* files because they’re too large for the netCDF file limit. The solution is to go to the nf_create call in src/proc_final_analysis.F90 and enable NetCDF’s …

…or, how to change your history interval mid-run for WRF. Here is a funny problem: I’m running a rather long WRF (or WRF-GC) case where I have to spin-up chemistry for about a month before I run the remaining time in the simulation. The spin-up period history output is no use to me, but …

GEOS-Chem has a long living conservative lat-lon to lat-lon regridder called Map_A2A. Despite formerly being a module from elsewhere (GEOS?), there is absolutely no documentation on the code, and thus it had bugs that were caused due to sometimes missing knowledge about the assumptions in the …

List of uncommon HEMCO errors This blog post is designed to house a set of highly obscure errors you may see in HEMCO. As always, if you see an error with HEMCO, check the HEMCO.log first! You may be looking at your model log and things are not as detailed there. HEMCO ERROR: STAT /= 0 If you see …

Summary This is a working draft guide for setting up WRF/WRF-Chem/WRF-GC on the Harvard Research Computing Cannon (formerly “Odyssey”) cluster. The guide is being actively updated and polished. Libraries module purge module load git/2.17.0-fasrc01 module load intel/17.0.4-fasrc01 module …

If you are running WRF 3.x series with the NCEP GFS data updated some time in 2019 you may have found an error along the lines of: ERROR: The mandatory field TT was not found in any input data. There may also be an error with metgrid.exe where you get: ERROR: Error in ext_pkg_write_field How to fix? …

If you are trying to run any I/O with netCDF, pnetCDF or hdf5 on AWS’s Lustre file system (FSx), you might encounter the following error and your program crashes: File locking failed in ADIOI_Set_lock64(fd B,cmd F_SETLKW64/7,type F_WRLCK/1,whence 0) with return value FFFFFFFF and errno 26. If …

Summary This guide is being actively updated as we prepare to publicly release WRF-GC. Stay tuned for updates. This is a tutorial on how to set-up the WRF-GC model on the Amazon Web Services cloud. There have already been successful efforts and guides on setting up WRF and GEOS-Chem on the AWS cloud …