- Qlustar General - Qlustar Mailing Lists

[Qlustar-General] Qlustar 12 (Ubuntu 20.04)
by randomtasks＠gmail.com 04 Jan '21

04 Jan '21

Hello. Back in June 2020, one of the news posts seemed to indicate that Qlustar 12 (with Ubuntu 20.04 support) was expected sometime in 2020. I've been eagerly awaiting this for months. Any word on when Ubuntu 20.04 will be supported? > This is the last feature addition to Qlustar 11. We now work at full steam on the > Qlustar 12 release based on Ubuntu 20.04 and scheduled for some time later this year. Thanks for any update! ~Rodney

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[Qlustar-General] OpenHPC 2.0/CentOS 8.3 on Qlustar 11
by Roland Fehrenbacher 04 Jan '21

04 Jan '21

The Qlustar team is pleased to announce the immediate availability of OpenHPC 2.0 [1] on top of CentOS 8.3 as an update to Qlustar 11. You can migrate your existing images and chroots to this new release in the usual way [1]. New ones can be generated via QluMan. Note that the disappearance of CentOS [3] as we knew it in the past, will not have a negative impact on Qlustar users running CentOS based nodes. There will be a simple migration path to whatever new RHEL compatible distribution will turn out to be the best choice at the end of 2021. Migration will involve nothing more than a usual Qlustar security update. [1] https://openhpc.community/openhpc-2-0-released/ [2] https://docs.qlustar.com/en-US/Qlustar_Cluster_OS/11.0/html-single/Administ… [3] https://blog.centos.org/2020/12/future-is-centos-stream/

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[Qlustar-General] update the invidia driver in chroot
by a.gabbana＠tue.nl 19 Dec '20

19 Dec '20

Hi, I would like to install cuda11 in a cluster. In order to do so, I would need to first install the latest nvidia driver 450. In bionic the default is the 440 version; is there any way to update to the latest nvidia driver? with best regards A.

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[Qlustar-General] Mounting an existing LV
by Ansgar Esztermann-Kirchner 07 Dec '20

07 Dec '20

Hello List, I'm wondering if anyone is mounting pre-existing (local) storage on a Qlustar node, and if so, how you go about it? My initial guess was to re-define the setup (xfs on LVM on mdraid) in the Disk Config assigned to the node, and mark it with preserve_always, but then the node refuses to boot correctly because setup-storage complains it cannot preserve my LV as it doesn't exist. I guess I could create per-node fstab stubs containing just the necessary lines, push them to the nodes using common/image-files with softgroups, and then add a common/rc.boot script to look for such stubs and mount them, but maybe there's a more integrated way? Thanks, A. -- Ansgar Esztermann Sysadmin Dep. Theoretical and Computational Biophysics http://www.mpibpc.mpg.de/grubmueller/esztermann

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[Qlustar-General] Security/Bug fix releases 11.0.1.4-b522f1319/21 / 10.1.1.17-b521f1318
by Roland Fehrenbacher 30 Nov '20

30 Nov '20

The Qlustar releases 11.0.1.4-b522f1319/21 and 10.1.1.17-b521f1318 are ready including a number of security and bug fixes. Please check the following web pages for details about security fixes and special update instructions: https://qlustar.com/news/qsa-1126201-linux-kernel-vulnerabilities https://qlustar.com/news/qsa-1126202-security-update-bundle This release also includes the following version updates: - Centos 7 version is now 7.9 - ZFS version is now 0.8.5

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[Qlustar-General] Security/Bug fix releases 11.0.1.3-b522f1314 / 10.1.1.16-b521f1313
by Roland Fehrenbacher 10 Oct '20

10 Oct '20

The Qlustar releases 11.0.1.3-b522f1314 and 10.1.1.16-b521f1313 are ready including a number of security and bug fixes. Please check the following web pages for details about security fixes and special update instructions: https://qlustar.com/news/qsa-1009201-linux-kernel-vulnerabilities https://qlustar.com/news/qsa-1009202-security-update-bundle

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[Qlustar-General] I subscribed to the mailing list, and posting, but not getting posted
by linux2cloud.consultant 11 Sep '20

11 Sep '20

Hi Admin, I have subscribed to the mailing list, I posted one introduction mail about me and what I am planning to with HPC but my mails are not seeing in the mailing list Can you please check Linux-AWS Consultant Sent with [ProtonMail](https://protonmail.com) Secure Email.

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[Qlustar-General] Hi, introduction new comer
by linux2cloud.consultant 10 Sep '20

10 Sep '20

Hi All, I am Saji. Just joined the mailing group. thought about say a HI, and a introduction about me. I have good Linux exposure and now working on AWS cloud based solutions. Very less experience in python programming, but picking it up. Very less knowledge or experience in HPC, have installed and configured OpenHPC, rockcluster, and now going to do Qlustar Recently me had idea to work on write up on comparing opensource HPC [OpenHPC, RockCluster, Qlustar] . I am waiting for my monster PC to be ready, so that I try out all three and do a comparison study . By this month end I will be assempling the required PC and working on it. Will be updating to the mailing lis tthe progress Thanks Saji Linux-AWS Consultant Sent with [ProtonMail](https://protonmail.com) Secure Email.

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[Qlustar-General] NFS boot scripts do not run
by stephanie.kerckhof＠ec.europa.eu 25 Aug '20

25 Aug '20

Hello, We are encountering problems with the NFS boot scripts. We already used this on another installation of Qlustar. It was working fine, but on our new install, it seems that the scripts are not executing at boot anymore. Here is the procedure we followed: 1. We created a script in /etc/qlustar/common/rc.boot 2. We made the script executable using chmod +x If I look on the node, the script is visible in the NFS folder /etc/qlustar/common/rc.boot. If I execute it manually, it has the behaviour I'm expecting from it. Do you have any idea of why the NFS scripts could have some problems in executing at boot time? I was also wondering if there would be a way to start a service automatically at boot on a node? Thanks already for your help.

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[Qlustar-General] Security/Bug fix releases 11.0.1.2-b522f1305 / 10.1.1.15-b521f1304
by Roland Fehrenbacher 22 Aug '20

22 Aug '20

The Qlustar releases 11.0.1.2-b522f1305 and 10.1.1.15-b521f1304 are ready including a number of security and bug fixes. Please check the following web pages for details about security fixes and special update instructions: https://qlustar.com/news/qsa-0821201-linux-kernel-vulnerabilities https://qlustar.com/news/qsa-0821202-security-update-bundle The following non-security related enhancements/bug fixes are included: + Fixes - The package openmpi-bin was not installable. This is fixed in an updated version.

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[Qlustar-General] Compute nodes do not boot
by Alexey Yaremchuk 12 Aug '20

12 Aug '20

Dear experts, I am trying to install a Qlustar OS on several Ethernet-linked machines and still compute nodes do not boot. The installer reports that there have been no errors, head and FE VM nodes do start, Qluman sees them and I could not find any error messages from dmesg except insignificant note that firmware load for regulatory.db failed. I installed a Debian system on one of compute nodes and upon configuring the network interface with a static address, established an ssh connection both with the head and VM-FE nodes. At least this ensures that cables are OK. If I configure it as dhcp, it does not discover dhcp server. If I force BIOS boot from the network, I receive either PXE-E51: No DHCP or proxyDHCP offers were received from Intel Boot Agent, if I make BIOS use only Legacy OpROM, or Media Present ... Start PXE Boot over IPv4 ... with a silent subsequent fall back into BIOS Setup, if I choose to use UEFI driver. I tried different combinations of Boot Device Control {UEFI_and_Legacy_OpROM|UEFI_only|Legacy_OpROM_only}, Boot from Network Devices {Legacy_OpROM_first|UEFI_driver_first}, OS TYPE {Other_OS|Windows_UEFI_mode} in BIOS Setup, and none of them worked. Qluman confirms that Boot network is configured as dhcp, and systemctl says that there are no failed services. Since I am the only one on the forum with such a problem, probably it can be fixed easily. However, I have no idea what to check and look forward for help. Thanks, Alexei

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[Qlustar-General] openmpi-bin
by marra＠irc.cnr.it 12 Aug '20

12 Aug '20

Dear Qlustar experts, I am facing a problem with the installation of software on the bionic chroot. I need to install a software called OpenFOAM (CFD simulations). It requires as a dependency the package openmpi-bin, but when I try to install it with the following commands: # chroot-bionic # apt install openmpi-bin I get the following diagnostic messages: Reading package lists... Done Building dependency tree Reading state information... Done Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: openmpi-bin : Depends: openmpi-common (= 2.1.1-ql.1) but it is not going to be installed E: Unable to correct problems, you have held broken packages. I have so tried to uninstall the already installed mpi packages (openmpi-common-4.0, openmpi-gcc, openmpi-gcc-4.0) hoping to fix the broken packages, but the result is exactly the same, I continue to get this error. The strange for me is that in the output of command: # apt list the openmpi-bin package is listed as: openmpi-bin/11.0-bionic 2.1.1-ql.1+11-bionic amd64 Then, after having removed all openmpi* packages already installed, I was sure that by using the command: # apt install openmpi-bin would have rebuild the correct dependencies and installed aligned openmpi packages. Instead I got always the same error. I think this could be a common issue so I decided to share my experience with the other Qlustar users. I would be very grateful to receive your hints. Best regards, Franco

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[Qlustar-General] nfs fails on compute nodes
by marra＠irc.cnr.it 12 Aug '20

12 Aug '20

Dear Qlustar experts, after a successful installation of the latest version of Qlustar (ver 11.0.1), I am facing a problem with the setup of computing nodes: they do not mount the nfs directories for apps and home. To me, everything looks correctly set up (checking with the qluman-qt application), Filesystem Exports and Network FS Mounts look correctly defined and assigned to the configs of the nodes. The only signal that something in the configuration of nodes is maybe not correct is an empty /etc/fstab, but probably the mount mechanism is different from standard mounts. What happens is that doing ssh to a compute node nor the apps nor the home directories are found. With the previous version 10.0 I did not have (on a different older cluster without IB) this issue. Please, can you give me some hints about what I have to check to fix this issue? Thank you in advance. Best regards, Franco

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[Qlustar-General] OpenMPI failure
by Kim Peterson 07 Aug '20

07 Aug '20

Qlustar Kim here again; new Qlustar user, local university CS student. I have installed Qlustar on a Master node with 2 compute nodes attached, and I have installed the QluMan GUI Singularity container on a stand alone Front End computer. All seems to be working well. I get to Section 1.8 near the end of the First Steps Guide, and follow the instruction to log into the User account I have set up on the Head Node (Section 1.7), and run a test to verify the installation of MPI. I get no response to the instruction mpicc.openmpi-gcc -o hello-world-c hello-world.c I note that I get a response of: "no such instruction found" when I try: mpirun --version Anyone have an idea of what I might be doing wrong or what I might do to get OpenMPI working? Kim

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[Qlustar-General] install qluman-qt fails
by Kim Peterson 22 Jul '20

22 Jul '20

I have set up a small cluster with a Master and 2 compute nodes. The Master has public and private Ethernet interfaces. The public interface is the connection to the internet. The private interface is the connection with the compute nodes. I installed Qlustar 11.0.1-0 on the Master, which completed with no issue. I had to restart the network services with systemctl restart systemd-resolved.service after the second re-boot during installation, and then proceeded with the First Steps checklist. I did not configure a Demo Cluster (Step 1.3) and I did not install additional software (Step 1.5). First Steps went fine up until step 1.6 "Running the Cluster Manager QluMan". Using the Head Node, I obtained a one-time token and saved it to /media/token (Step 1.6.1). When I attempted to install QluMan (Step 1.6.2), the review of packages that appeared on the monitor was normal looking, but the installation of each package failed. Failure indication was the same for each package to be installed; There was a notice that started with "Failed to fetch http://repo.qlustar.com/repo/ubuntu/pool/ ..." and ended with "... temporary failure resolving "repo.qlustar.com". I did a little communication check of the public network: ping www.google.com produced "Temporary failure in name resolution" ping 8.8.8.8 produced a steady stream of reports of "64 bytes from 8.8.8.8: icmp_seq=<n> tt1=116 time = 78.2 ms", with <n> incrementing each time. I also note that when I power up the 2 compute nodes after the successful Qlustar installation on the Master, there is no booting going on, which I presume may be related to whatever has made the Master unable to resolve network ip addresses and names. I am a CS student working a project that required a small cluster computer, so I have no particular skill with the technology here. I spent the better part of the day trying to figure out what I'm doing wrong, but I have failed. The issue is reproducible. I have done multiple installs from scratch and always get the same result. I note that the Qlustar OS installation and the early First Steps require access to the Qlustar.com repo, and that the "Final Reboot" at Step 1.2 appears to be when the Master node loses its ability to resolve network addresses and names and becomes unable to access the Qlustar.com repo. Do any of the kind listeners recognize my error or perhaps could recommend some sequence of steps I might take to isolate the problem? Kim

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[Qlustar-General] Security/Bug fix releases 11.0.1.1-b519f1302 / 10.1.1.14-b521f1301
by Roland Fehrenbacher 16 Jul '20

16 Jul '20

The Qlustar releases 11.0.1.1-b519f1302 and 10.1.1.14-b521f1301 are ready including a number of security and bug fixes. Please check the following web pages for details about security fixes and special update instructions: https://qlustar.com/news/qsa-0715201-linux-kernel-vulnerabilities https://qlustar.com/news/qsa-0715202-security-update-bundle The following non-security related enhancements/bug fixes are included: Qlustar 11.0.1.1-b519f1302 updates to/adds + the latest Lustre LTS release 2.12.5 + the latest Nvidia graphics drivers 440.100 supporting recently introduced Nvidia hardware + Several Nvidia GPU metrics (temperature, load, fan) were added to Ganglia + Fixes - QluMan * Improve slurm job information updates on busy head-nodes * Allow multiple networks for external hosts in Filesystem Mounts * Fix exceptions when editing properties - GPU detection (possibly missing /dev/nvidia-uvm on hardware with many GPUs) - NIS was failing in certain situations due to wrong /etc/hosts

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[Qlustar-General] PXE problems since update
by stephanie.kerckhof＠ec.europa.eu 09 Jun '20

09 Jun '20

Hi, We recently tried to update qlustar to the 11.0.1 version adding UEFI support and CentOS 7.8. Since then, we got several problems with dnsmasq. First, the directory /var/lib/tftpboot/ was missing so we created it manually and added symbolic links to the files specified in the administration manual section ⁠4.1.2. It solved part of the problems we had, but now, while running systemctl status dnsmasq, we get the following error: dnsmasq-tftp[1758]: file /var/lib/tftpboot/grubnet.i386-pc not found Could you tell us where we could find this file? Thanks in advance for your help.

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[Qlustar-General] login-c and beo nodes do NOT start
by mauro.delossantos＠udc.es 04 Jun '20

04 Jun '20

I´m deploying a head-node in a Virtualbox VM with a FE VM and 2 demo nodes (beo-01/2). After follow the doc guide's instructions, i have the head node up with perfect state but login-c and beo nodes couldn't get started. Anybody knows the reason and how to fix that? Thanks.

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[Qlustar-General] 11.0.1 adds UEFI support and CentOS 7.8
by Roland Fehrenbacher 03 Jun '20

03 Jun '20

The Qlustar team is happy to announce the immediate availability of Qlustar 11.0.1 for download [1]. This minor release has two new features: a) Full UEFI support for the Qlustar installer and PXE booting of nodes. b) The move to CentOS 7.8 as the new supported minor CentOS 7 version. The Qlustar installer now transparently supports installation on legacy PC BIOS hardware as well as machines running under UEFI. If you have the choice, we recommend using the UEFI mode on your hardware. Our PXE booting mechanism has been doubly revamped: Firstly, we use GRUB as the boot loader now per default and secondly, we fully support UEFI based hardware transparently. So it will not matter whether your hardware runs under UEFI or PC BIOS, it should just boot fine, once registered correctly under QluMan. Reverting to booting with PXELINUX on PC BIOS machines is supported if needed/desired. Please follow the special update instructions [2] of the latest security announcements when updating and if you use QluMan singularity images, make sure you download [3] the latest version. This is the last feature addition to Qlustar 11. We now work at full steam on the Qlustar 12 release based on Ubuntu 20.04 and scheduled for some time later this year. [1] https://www.qlustar.com/download [2] https://www.qlustar.com/news/qsa-0527201-linux-kernel-vulnerabilities [3] https://www.qlustar.com/download

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[Qlustar-General] Security/Bug fix releases 11.0.1.0-b519f1296 / 10.1.1.13-b521f1295
by Roland Fehrenbacher 30 May '20

30 May '20

The Qlustar releases 11.0.1.0-b519f1296 and 10.1.1.13-b521f1295 are ready including a number of security and bug fixes. Please check the following web pages for details about security fixes and special update instructions: https://qlustar.com/news/qsa-0527201-linux-kernel-vulnerabilities https://qlustar.com/news/qsa-0527202-security-update-bundle

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[Qlustar-General] CentOS 8 support has arrived
by Roland Fehrenbacher 20 Apr '20

20 Apr '20

CentOS 8 support is now available as a third Qlustar edge-platform and was published together with the latest security updates. It comes with the same functionality as our CentOS 7 port which includes out of the box OpenHPC 1.3.9 integration, Slurm 18.10.x, up-to-date Nvidia 340.x drivers, Lustre client and BeeGFS client. Making your compute nodes switch to CentOS 8 on an existing Qlustar cluster installation is extremely simple: First create a CentOS 8 chroot [1] optionally adding OpenHPC base support, then generate a CentOS 8 OS image [2] selecting the modules you require and finally a boot config [3] using the just generated image. After assigning [4] this boot config to the nodes you want to run it on, you just need to reboot them and voilà your CentOS 8 nodes are ready to be used. Note that OpenHPC 1.3.9 was originally built for CentOS 7.7. We had to make a few adjustments to make the OpenHPC parts relevant to Qlustar (compilers, MPIs, library packages and applications) work for CentOS 8. The OpenHPC test-suite was run successfully against these components. Once OpenHPC 2.0 will be out, we'll publish instructions to update to it. This will be straightforward. Additional improvements with this release: Updates to the latest Lustre 2.12.4 LTS release and the newest Nvidia graphics drivers 340.64 adding support for the latest Nvidia GPUs. These two updates apply to all Qlustar 11.0 platforms (Ubuntu 18.04 and CentOS 7/8). [1] https://docs.qlustar.com/en-US/Qlustar_Cluster_OS/11.0/html-single/QluMan_G… [2] https://docs.qlustar.com/en-US/Qlustar_Cluster_OS/11.0/html-single/QluMan_G… [3] https://docs.qlustar.com/en-US/Qlustar_Cluster_OS/11.0/html-single/QluMan_G… [4] https://docs.qlustar.com/en-US/Qlustar_Cluster_OS/11.0/html-single/QluMan_G…

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[Qlustar-General] Trying to sort network interfaces: can I shell out in the installer?
by jarett＠bioteam.net 15 Apr '20

15 Apr '20

There are six relevant network interfaces on my head node, some of which are relevant and linked and some of which are not, and I can't tell which is which from the network interface names and am not on site to plug and unplug things. Is there some way to shell out, bring all the interfaces up and puzzle it out that way? TIA.

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[Qlustar-General] Security/Bug fix releases 11.0.0.8-b518f1287 / 10.1.1.12-b521f1292
by Roland Fehrenbacher 14 Apr '20

14 Apr '20

The Qlustar releases 11.0.0.8-b518f1287 and 10.1.1.12-b521f1292 are ready including a number of security and bug fixes. Please check the following web pages for details about security fixes: https://qlustar.com/news/qsa-0406201-linux-kernel-vulnerabilities https://qlustar.com/news/qsa-0406202-security-update-bundle The following non-security related enhancements/bug fixes are included: * Qlustar 11.0.0.8-b518f1287 updates to + the latest Lustre LTS release 2.12.4 + the latest Nvidia graphics drivers 440.64 supporting recently introduced Nvidia hardware

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[Qlustar-General] Cannot add nodes from DHCP detect / how to authenticate users via Active Directory? / how to add my "scratch" NAS?
by Jarett DeAngelis 19 Feb '20

19 Feb '20

Hi folks, I was able to get my head node installed and can now boot it via the YUMI Linux installer USB. (I still don’t know why this is necessary, but hey, it works.) Now I have two issues: How do I add nodes to the cluster? I tried doing this with qluman-qt. I go to Manage Hosts and New Hosts, where it sees the MAC from one of my nodes. If I try to add it to the cluster I get a SQL error from Python about how it cannot insert a new record without the “status” field. Like so: If I click either “Add Selected” or “Add Host” here, I get this: Which seems to be generated from this SQL insert: The procedure for adding hosts actually doesn’t seem to be documented anywhere. I thought maybe I could try it from the command line, but there also doesn’t seem to be any documentation for the qluman-cli utility. I’m not entirely sure how the host abstraction works in Qlustar. My front-end/head node’s hostname is “argo,” yet the only thing in the host database visible in qluman-qt that seems to map to this is “beosrv-c.” Where did that name come from? The next steps I would like to get to are as follows: Add my two compute nodes to the cluster Add the NFS NAS I built to be a “scratch” filesystem available across all nodes Install some bioinformatics software (a good resource for this in Qlustar would be a big help) Make the cluster able to authenticate users via an Active Directory instance — I have a hard time understanding users in Qlustar. There is a very brief blurb in the administration guide about sssd.conf being replicated to each machine in the cluster, but the hostname in SSSD would have to be different for each node, so I don’t think that works for AD unless Qlustar is doing some kind of templating with the names. The other issue here is that when you join Linux machines to Active Directory and users log in, no entry is created in /etc/passwd, so if user process work is being kept track of with those, it won’t work. Unless the typical method for authenticating users is to use “plain” LDAP somehow without actually performing an AD join and just manually creating users that are then only authenticated against LDAP, and replicated between hosts normally because they’re “regular” UNIX users? That would also be fine; the problem here is that I can’t figure out how users are supposed to work. I added a user via qluman-qt and it appears not to have been added to /etc/passwd either, and since I have not yet configured SSSD I can’t figure out what those users are for. I can’t log in to SSH with them. I know that’s a lot at once; TIA. Jarett

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[Qlustar-General] Re: Can't install
by Roland Fehrenbacher 19 Feb '20

19 Feb '20

>>>>> "J" == Jarett DeAngelis <jarett(a)bioteam.net> writes: J> I mean it just isn't an option. The attached is what I get if I J> turn UEFI options off entirely. It doesn't recognize the drive as J> bootable. If I turn UEFI options on, the USB drive is there, but J> of course doesn't work. Have you turned 'secure boot' off? If not please try that.

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